The German (Omega Pharma – Quick-Step) attacked over the top of the final climb and held off his rivals for upwards on 20 kilometres to take the victory by 46 seconds on the chasing pack.
Seven riders gave chase following the second category ascent, Francesco Gavazzi (Astana) getting the best of the bunch sprint ahead of Eros Capecchi (Liquigas-Cannondale) into Mentougou.
A short, reduced-length stage saw attacking from the very start, with the race splitting to pieces on the opening first category climb.
That set the tone for the day with groups strewn across the parcours, Martin proving the strongest as he opened up a 50-second lead over Gavazzi.
Edvald Boasson Hagen retained fourth overall for Team Sky as he finished in the second chase group on the road.
After a straightforward opening criterium on day one, the introduction of more climbs had the desired effect as the race blew apart.
Kicking off at the Bird’s Nest Stadium, scene of Tuesday’s opening sprint finish, 126km lay in front of the riders as the race went in search of climbs.
Five riders combined to go clear early on, making up 3:15 on the bunch, yet surprisingly the gap plummeted as the race hit the first climb of the day.
The first category ascent split the peloton to pieces, a select group heading clear with Dan Martin (Garmin-Sharp) and Tony Martin the most prominent names to hit out and open up a gap.
With both Martin’s reeled in the lead group were motivated to keep their gap to the group behind, Euskaltel-Euskadi and AG2R La Mondiale pushing the pace onwards to peg the margin at around the 1:30 mark.
Tony Martin attacked out of the darkness, plummeting down the descent to remain clear for his first non-time trial stage victory for two and a half years.