Harry thinks initially, based on the said teacher's behaviour, that it is indeed Professor Severus Snape who maybe working with Lord Voldemort to steal the Sorcerer's Stone. However, his suspicion is revoked by the startling revelation that Snape was, indeed trying to protect Harry by keeping the stone from Professor Quirrell, the then Defence Against the Dark Arts teacher, who was the one working with the Dark Lord, not Snape. It seemed that Quirrell had a part of Voldemort within him, which forced him to obey the Dark Lord' wishes.
Harry, at first, believes Severus Snape is the teacher who was working with Lord Voldemort (he who must not be named). However, the irony was that it wasn't Snape - Snape was trying to protect Harry. Instead, it was Professor Quirrel, who wasn't just helping Voldemort, but he was hosting Voldemort on the back of his head.
Through the majority of the novel, Harry thinks that the Snape, the Potions professor, is in league with Lord Voldemort. Snape displays all the classic signs of being a villain. He is described as always dressing in black, "stalking" (or something similar) rather than walking down corridors all the while in a bat-like manner, being overly harsh to his students, and giving off a confident/mysterious/powerful/frightening aura. Undoubtedly many readers were like Harry in thinking that Snape serves the most evil man in the Wizarding World.
From the very beginning, Harry suspected Snape of working with Voldemort. That's because he thought his scar hurt when he saw him. In actuality, it was because he saw Quirrel but like Quirrel said, "Who would suspect poor st-stuttering Professor Quirrel?". This won't be the first time Harry suspects Snape, and it won't be the first time he's wrong.