The fifth seed blasted 43 winners to Ferrer's 14 and, although he tightened a little in the final game, got home on his third match point in just over two hours and was always in control of the match.
Ferrer usually drags his opponents into long rallied and generally wears them down, but Nishikori showed himself to be up to the task and won most of the longer rallies.
"I'm always ready to play five sets against him so I was surprised to win in three," Nishikori said after the match.
"I've had three good matches here and have been hitting well so I had a good game."
Japan's number one will next meet defending champion Stan Wawrinka for a place in the semi-finals.