Nadal will be battling against big-serving John Isner in the quarter-finals.
The Spanish tennis maestro, who is bidding to win his second China Open title, remained dominant throughout the match as he eased past Khachanov 6-3, 6-3 in a one-sided men's singles second round that lasted nearly one and a half hour.
"Happy about the match today", said Nadal. Tomorrow (Friday) will be a tough one against Isner.
The US Open champion is looking to maintain his place at the top of the world rankings ahead of November's ATP World Tour Finals, and an extra step has been taken with a 6-3 6-3 victory over Khachanov.
Like Nadal, Zverev is bidding for his sixth title of the year.
"He played so aggressive, having a lot of success, hitting a lot of winners, returning very well".More news: Rahul unquestioned choice to lead Congress: Randeep Singh Surjewala
'Everybody knows that he serves huge and it is so hard to break him.
Nadal broke Khachanov in the fourth game of the opening set and never looked back as he recorded a 6-3 6-3 win.
He is looking to go on and make the semi-finals for the second time.
In the women's tournament, Jelena Ostapenko advanced after Peng Shuai, the last Chinese player in the competition, retired from the match while trailing 3-0. The German will play Andrey Rublev in the next round, who defeated seventh-seeded Tomas Berdych 1-6 6-4 6-1.
She is now in 10th place and winning the China Open will help her overtake eighth-placed Briton Johanna Konta, going into the penultimate week of the season.
The American has so far beaten Malek aziri and Leonardo Mayer to reach the quarter-finals.