Nadal dropped a set to Lucas Pouille in his opening match and once again started slowly, saving there break points in his opening service game.
But the world No 1 eventually took control, winning the first set in 44 minutes and taking just three minutes longer to wrap up the second by the same scoreline, breaking Khachanov for the third time in the match to seal an emphatic victory.
Nadal will now face big-serving American Isner in the quarter-finals after Leonardo Mayer earlier in the day for the loss of just three games.
More to follow.