When someone uses Polyjuice Potion, their voice changes along with their body. Therefore Crouch Jr. would sound just like the real Mad-Eye.
In the film version of Harry Potter and the Chamber of Secrets, Polyjuice Potion does not cause the drinker's voice to change as well as their appearance. However, Barty Crouch Jr's voice does change to Moody's in Harry Potter and the Goblet of Fire (film). However, it is possible he could have just been imitating Moody's voice. It does say, however, in the book version of Chamber of Secrets, that Harry, Ron and Hermione's voices change after taking it. If Polyjuice potion doesn't modify the voice them they may have used a spell.