Murray played some sublime tennis at times as he wrapped up a 6-3 6-3 6-1 victory to reach the semi-finals of the Australian Open for the third successive year.
Nishikori, who came through a five-set epic against sixth seed Jo-Wilfried Tsonga in the previous round, desperately tried varying his game but he could find no answer to Murray's play.
However if there was one thing that did let Murray down at times it was his service game - with the 24-year-old broken twice.
Murray broke back immediately on each occasion, though, to limit the damage.
"It was a good match, a lot of fun points, most of them he was winning so I was trying to keep them as short as possible," Murray said.
"But I need to serve better. I didn't serve particularly well but the returning was good so that was a positive.
"My game has been getting better each match and I am moving better and I am going to be fresh going into the weekend."
Nishikori, the first player from Japan to reach the last eight at Melbourne Park in 80 years, had spurned five break-point opportunities in the opening set.
The Scot, though, was even more wasteful as he missed eight opportunities - however the one he did take was enough for him to seal the set.
Murray broke at the start of the second set - only for Nishikori to hit back immediately, although he almost let the world No.4 off the hook as two chances passed him by before he finally levelled.
Nishikori's joy was shortlived, though, as Murray broke twice more to move into a two-set lead.
The 22-year-old looked out on his feet at the start of the third set as Murray moved 2-0 up - although a couple of double faults allowed Nishikori to break back.
Yet again Nishikori, though, failed to take advantage as Murray moved 3-1 up before accelerating away to wrap up the set and the match.