Speaking at a fundraiser, she said they were "racist, sexist, xenophobic, Islamophobic - you name it".
She then went on to say the rest of the Republican nominee's supporters were "just desperate for change".
Mr Trump's campaign manager said Mrs Clinton had insulted "millions of Americans", with her comments.
Polls released earlier this week suggest Mr Trump is gaining on Mrs Clinton, and the rivals are neck-and-neck in the key battleground states of Ohio and Florida.
In other developments: