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He learned it during his time with the Dursleys. He avoided many unwarranted beatings from Vernon Dursleys just by looking at the man's mood. Plus by observing Dudley Dursley, Harry knew where to hide himself to avoid his cousin, other than the library. Dudley always avoided the library, but that didn't mean Harry liked reading.
For example, whenever Ron Weasley asks Harry for a chess match, he usually is feeling upset or insecure and wishes for a confidence and morale boost. That's not even talking about Ron wanting to talk about the Chudley Cannons, he is bottling up emotions and likely wishes to vent something but never has the courage to do so.
Meanwhile Hermione Granger lightly smacked people on the head whenever someone did something she perceived as wrong or stupid, especially to people close to her. She likely did something her parents did to her often and she picked up accidentally. Or when Hermione constantly studies and reviews material that teachers wouldn't get to in weeks, if not months. Her parents likely were disappointed in Hermione for a test or something similar. Hermione did not wish to feel that disappointment ever again.
Perhaps observing and noticing his own best friends would be easy. Harry did spend most of his time with them after all.
Neville Longbottom may be a friend, but definitely not as close. Harry notices the way Neville talked about plants too easily to deduce that Neville treated it as his hobby, and even his safe haven. Professor Sprout also being kind to the boy only contributed to this more. Very unlike Severus Snape, which makes Neville's hands shake slightly even at the sight of him.
Talking about Severus Snape, there was a lot to observe from the potions professor despite the usually indifferent mask he constantly wears. The fact that he does such is already telling of much. Snape was hiding, constantly, almost as if in fear of something. To the point there is always slight hesitation to even eat in the Great Halls. Also, although it may not be a secret the man has an unreasonable amount of hatred for Harry, it definitely is a secret to why he hates Harry. Or, at least supposedly.
Everyone says Harry looks like his father, except for the eyes, which is his mother's. Snape never exactly looked into Harry's eyes. Well except for a few times, but always did Snape, of all things, paused before taking an abnormally large amount of points, even for being the Gryffindor boy-who-lived. It's strange how Snape would even yell at Neville, boring his eyes into him to instill more fear, and yet not use it against Harry.
Therefore, Harry believes Snape may not actually hate his mother, but definitely hate his father. The way every time Snape sneered and spat Harry's last name out as if it was an insult in itself supported this observation as well.
Talking about Snape, the Head House of Slytherin, there is no way in bloody hell Harry isn't observant of Draco Malfoy. Malfoy practically follows his House Head around like a bloody pet constantly with his eyes. Excluding potions, but that's when Snape pays attention to Malfoy, where Malfoy gets his approval. The number of points given to Slytherin for potions completed by Malfoy is outrageous. It's around all the other Slytherins getting points in potions together and then doubled.
And the amount of times Harry overhears Malfoy bragging about his points to his housemates and Malfoy brags to Harry as to mock Harry is twice per day, at least. No wonder Gregory Goyle and Vincent Crabbe are the only ones that stick with Malfoy. They're getting paid to do that by Malfoy's father.
And on his father, does Malfoy go on and on about. He'll probably say he'll tell his father about something, which happens without fail every single class Harry has with him and during every time students and staff eat.
From all of this, Harry just purely infers Malfoy definitely has daddy issues to the point he is deluding himself that his father would pay attention to him, while it is probably not going to happen. Or perhaps Malfoy is sometimes imagining Snape as his dad. Honestly, that would be absolutely believable.
Anyhow, when Malfoy is a literal blabbermouth that would not stop talking about his father, Theodore Nott just doesn't. Nott stays close with Malfoy, but he is always uninterested. He even shuffled away from Malfoy and flinches, especially at the start of the year, whenever Malfoy mentions his father. It isn't too far-fetched that Nott is likely in a bad relationship with his father as well.
Honestly most Purebloods have familial issues. Blaise Zabini has a mother that keeps murdering her husbands. Ron has a family that does not care for each member remotely equally remotely. Ginny Weasley got all the attention as soon as she was born. Ron being so closely born to her, had mostly no attention. Percy Weasley drives himself to perfection to gain some attention in the family. Meanwhile, the twins do their pranks.
Malfoy and Nott have major daddy issues, as already said. Goyle and Crabbe have some serious familial issues considering their families are willing to sell them to the Malfoy family practically. The Greengrass sisters have issues with their parents, considering they constantly stick together and look around and observe their surroundings. Pansy Parkinson has absent parents, considering how much she looks up to Snape and she sometimes looks disappointed whenever Snape compliments Malfoy.
Professor Minerva McGonagall is also hiding something, despite what most believe. She always looked slightly guilty whenever looking at Harry. Perhaps a deep guilt for failing to keep her two favored students, Lily Evans and James Potter, alive.
Harry not only noticed about teachers and classmates, however. He also noticed some secret and not so secret things about the headmaster. Everyone knows Albus Dumbledore likes lemon drops and is addicted to the citrus hard candy.
The thing that they don’t know well is that there are three separate batches he has. Ones drenched in calming draughts, ones dipped in Veritaserum, and normal ones. Harry only knew that as he had each of them before on different occasions after all. Dumbledore often ate lemon drops from the batch with nothing. However, he always did act calmer after he ate one. Harry suspects it might be a placebo for the headmaster.
“Harry, are you dozing off again?” asked Hermione, who smacked Harry's shoulder lightly and completely interrupted Harry's thoughts.
Harry blinked a few times before his eyes actually focused on his friend. “Sorry, what were you saying?”
“I was trying to ask you if you found anything about the Philosopher's Stone yet,” sighed Hermione.
Oh yeah, that's why Harry dozed off. He, of course, knew what the Philosopher's Stone was. He could do a solid three minutes of details on that thing.
Harry shook his head. “Did you?”
Hermione frowned. “No, but let's keep trying.” She turned away and walked off back into the bookcases.
Harry knew about the Philosopher's Stone, and the rest of his years too, although not as clearly. He simply decided to pass the time to observe.
Most of the things he observed are so obvious now, especially when the tidbits of information that his mind flashes him about the future.