My story includes a magic school wherein students aged 12 learn magic. The sorting Is based on abilities, Meaning that if a student has thirst for dark arts, there most concentrated subject becomes dark arts and so. The students learn wand and hand magic. The mc and his friends discover the school secrets in book 1. My main question is that will people always compare a magic school idea to Harry Potter despite of changes? Will people read a book on Magic School?
Like it or not, there are some stories that have popularized a trope to such a degree that you can't escape from them. Like 1984 or Brave New World did for dystopias. Or Harry Potter did for magic schools.
Indeed, you can't even write a school for supernatural beings book series in general without being compared to Harry Potter. Vampire Academy, Rosario + Vampire, and House of Night are about schools for supernatural creatures, with little of the trappings unique to Harry Potter like actually learning magic. They still get called "Harry Potter but with vampires" anyway. Other magic school stories like The Worst Witch, The Magicians, and Little Witch Academia are also frequently compared to Harry Potter, despite The Worst Witch predating Harry Potter by decades.
There are some stories that, if writing in a certain subgenre, you just can't escape the shadow of.
There may come a time when people no longer think "Harry Potter" when they see a magical school story. But this probably isn't helpful to you.
Over a hundred years ago, Oliver Wendel Holmes Sr., poet, lecturer, essayist, doctor (and eventually the father of the famous supreme court justice) wrote a book called "Elsie Venner", with the titular character having a dangerous, snakelike personality because her mother had been bitten by a rattlesnake while pregnant with her. This conceit was introduced as a way to discuss original sin, but there's something very evocative about the idea of someone gaining the attributes of an animal from a "magic" bite. This was once a well-known book.
I'll give about fifty-fifty odds that you already thought of Spiderman. Now everyone knows about Spiderman, and basically no one has heard of Elsie Venner.
Do you want Magical School stories to not be compared to Harry Potter anymore? Just write the "Spiderman" of the magical school genre, and if people haven't already forgotten Elsie Venner, er, Harry Potter, they just might. Or rather, more likely, someone else will write "Clavius Melodram Finds His Way", or whatever, and you'll go from your stories being compared to Harry Potter to being compared to Clavius Melodram.
Depends on how long they've been reading.
When I first saw the Harry Potter books and movies, I compared them to Ursula K. LeGuin's A Wizard of Earthsea, a significant fraction of which centered around Ged's time in the School of Wizards on Roke ("at the center of the world"). In today's world, however, there are probably a hundred times as many people who have read the Potter books or seen the movies, as who have read the excellent Earthsea books. Others might think of the correspondence course from Bedknob and Broomstick either the two books, or the Disney movie that combined them. Or Diana Wynne Jones's Howl's Moving Castle, though the school was very much a minor side note in that. Brakebill's, the college in The Magicians, was billed as "Harry Potter but for adults". And never mind that the only similarity was a school dedicated to teaching magic.
But with a series that went above and beyond those (including the ones that were decades earlier -- Earthsea dates to the 1960s and Bedknob and Broomstick to the 1950s) to become a multi-billion dollar franchise, there's no way to avoid the comparison. If you want to distinguish yourself from Potter and Hogwarts, you need a more different world -- not just Hogwarts with twelve houses and more elective coursework.