The former US Open finalist reeled off five games in succession to take the opening set.
Nishikori, who is set to make his third appearance at the end-of-season Tour finals this month, reeled off five games in succession to take the opening set.
The former US Open finalist twice dropped serve early in the second set but earned a crucial break at five-all to set up a potential showdown with home favourite Jo-Wilfried Tsonga in the next round.
"I'm not thinking, you know, about 500 or 1000 wins," said Nishikori, who missed out on the milestone Sunday after he lost to Marin Cilic in the Basel final.
"I think this year has been pretty good. I have been winning a lot of matches and playing a lot of tournaments.
"Every year I feel like I'm getting strong so I'm happy with my performance right now."
Nishikori, 26, also finished runner-up to Novak Djokovic at both the Miami Masters and Toronto Masters earlier this year.
Belgium's David Goffin remained in contention for a London berth after he defeated Frenchman Nicolas Mahut 7-6 (7/5), 6-3 in round two.
The eighth seed currently trails Dominic Thiem, Cilic and Tomas Berdych in the race for the final two places in London.