I've only read the short story.

But according to wikipedia, one big difference in the novel is the addition of a subplot about a second woman that Charlie becomes romantically/sexually involved with. (As his intelligence increases, his libido "awakens," and he starts to fall in love with his attractive young teacher, Alice Kinnian. His new sexual feelings for Miss Kinnian are referred to in the short story, but in the novel, he later meets a second woman -- she's a fun-loving "шлюха" who is quite unlike the academically-minded Miss Kinnian.)

Ultimately, both women have great difficulty dealing with the rapid changes in Charlie's personality and intelligence, though their reactions are different, just as their personalities are different.