The 24-time Grand Slam champion battled back from a set down to beat local hope and world number 104 Bu Yunchaokete 4-6, 7-6(2), 6-2 in the last 16 in Beijing, extending his perfect record at the tournament to 31-0.
Djokovic, who returned to the ATP 500 event after an 11-year absence as he seeks to regain momentum following his exit from the top 10, is aiming for a strong finish to a season that included a shock first-round loss at the US Open, his earliest Grand Slam defeat since the 2006 Australian Open.
The 39-year-old Serb vomited midway through that match and was troubled by back and shoulder issues that affected his serve late on. He had also required a medical timeout during his opening-round victory over Portugal's Nuno Borges in Beijing.
"I don't want to go into details because then it's going to sound like I'm whining about something or looking for excuses," Djokovic told a news conference.
"Truth is that this year has been a big, big struggle for me with few particular issues that I've been having. I've been just trying to find different ways to be at least giving myself a decent condition physically and health-wise to be on the court and compete with the player across the net.
"Most of the matches and tournaments this year that I've played have been a real, real struggle for me physically. That's nothing to do with stamina. People mix it up. It's not stamina. It's something else. More related to health."
Djokovic did not elaborate on the problem but said he and his team were still trying to get to the root of it.
"Actually, surprisingly something I haven't experienced this year so far, that in the third set I kind of broke through. I felt better. Towards the end of the second and all third set, I felt fresher than I have in the beginning of the match...," he added.
"It's not fun when you're feeling like that on the court because then I'm investing my emotional, mental energy, and physical of course, more on the issues that I'm having rather than thinking about the game and how I can beat my opponent."
Djokovic has won a record six China Open titles, most recently in 2015 before making his return to the tournament this season.