Nishikori, who lost to Novak Djokovic in last year's Miami final, will face Italian Fabio Fognini who defeated American Donald Young 6-0, 6-4.
Another American, 13th seed Jack Sock, did make it to the last eight however, beating compatriot and qualifier Jared Donaldson 6-2, 6-1.
Sock will play the winner of the clash between fifth-seed Rafael adal, seeking his first win at Miami, and France's Nicolas Mahut.
Later on Tuesday, in-form Roger Federer, who has won the Australian Open and Indian Wells this year, is up against Spain's Roberto Bautista Agut.