The world number one got off to a poor start against the eighth seed, but ultimately won with a degree of comfort, triumphing 2-6 6-1 7-6 (7-0) 6-1.
For Stan Wawrinka the match 1/4 final against Marin Cilic has suddenly become a cakewalk - champion Roland Garros-2015 easily passed the Croatian giant and has extended its series of semi-finals in Paris three seasons.
Wawrinka is confident he can reverse the result of last year's semi-final here, when Murray won in four sets before losing to Novak Djokovic in the final. Previous year he was also playing really well and I had to play one of my best matches on clay to beat him.
Murray said: "Physically, I feel great".
Paris: Andy Murray vented his frustration at a lack of consistency from umpires after receiving two time violations in Wednesday's win over Kei Nishikori at the French Open. "You know, I'm the odd one out in the semis, but hopefully I can keep it up". He's great player. Very smart tennis player.
Murray said: "Obviously for a couple of points after that I was sacked up, because I was frustrated at that moment".More news: Kingpin in Tehran Terror Attacks Killed
"Paris has also had some problems too in the past year or two. From there I started to do a bit better". Anyone can win matches when they are playing well.
"The fourth, I think it was ideal tennis I played".
Echoing similar views, former Wimbledon champion Goran Ivanisevic said that although Murray started the tournament searching for form, he has managed to bring himself back on track as the French Open progressed.
"He played very well (against Khachanov) and he's playing better and better. It was windy, so the timing was hard, but once I was able to get into a rhythm and keep him away from the baseline, that made the difference".
"Obviously for a couple of points after that I was sacked up, because I was frustrated at that moment", said Murray.
After his win over Nishikori, Murray will face Stan Wawrinka, with Nadal taking on Dominic Thiem in the other semi-final. The third was a bit lucky for me, it helped that I was able to break him in his first service games in the last two sets. "But I don't know how much [effect] it had. It's never easy, and I think this week he's been playing well". And also, the fact I have a solid track record, winning tournaments, Grand Slam tournaments, and that really helps.' You are the oldest semifinalist since Jimmy Connors back in 1985.
But the second set proved the turning point for the double Olympic gold medallist, levelling up the match with the tennis that has taken him to top spot in the world with a 6-1 set.