The Omega Pharma-Quick Step rider came home 46 seconds clear of a seven-man chase group at the end of a 126km stage from the Bird’s Nest Olympic Stadium to Mentougou.
The German was prevalent all day and attacked on a descent, following the final climb of the day, and powered home to take the overall lead in the last World Tour race of the season.
Mathias Frank (BMC), Maxim Belkov (Katyusha), José Iván Gutiérrez (Movistar), Juan Manuel Gárate (Rabobank) and David Tanner (Saxo Bank) formed an early escape and led the peloton by 2:40 after 60km.
But the gap was quickly whittled down on the 10.8km category one climb that came midway through the stage where an elite group of around 20 formed including Ireland's Dan Martin and Giro d'Italia winner Ryder Hesjedal.
That group split on the third and final climb of the day, a 5.4km category two ascent, and world time trial champion Martin made his move shortly after the summit with 26km remaining.
Francesco Gavazzi (Astana) led the seven chasers over the line and is second on GC, 50 seconds behind the leader.
"I came to China to try to get a good result, even if there was no TT this year," Martin said.
"I knew I had to try something without the TT. I knew, in the right moment, I had to take a chance. Today I felt good. There was a tough climb at the beginning, but I passed it without problem. About 25km from the finish there was a little downhill section after the climb. I turned and saw I had a small gap between me and the rest of the group, so I decided to go.
"Then, I did my own time trial giving my best - it worked in the end. It's super nice, especially for me because it is unusual to win a road stage. I am always happy to win the time trials, but it is quite amazing for me to win a stage like this. I feel good.
"Tomorrow it will be a question of tactics. We can't let the dangerous breaks get away, and we have to manage the race. We have a good team here, so for sure we will do our best. I have a 50 second lead in the GC, but now we will see the competitors.
"All the riders in the top 10 are dangerous. Some are climbers, some are sprinters who will take advantage of the bonifications and go for the final sprints. It will be a fight, but we will do our best to protect the leader's jersey."
All 18 WorldTour teams and the Chinese national team line up in the second edition of the five-day race.