The German time trial specialist, who also defended his 2011 world title in Limburg last month, completed the 48.5km course in 58:07, 41 seconds ahead of Omega Pharma-Quick Step team-mate Sylvain Chavanel.
BMC Racing Team’s 22-year-old American Taylor Phinney was third, one second behind Frenchman Chavanel.
French pair Jeremy Roy and Lazlo Bodrogi - the 2007 winner - were fourth and fifth respectively.
"It's a nice way to finish the season," Martin said. "When you win it's always good, I did the same even last year closing my season with a victory here.
"Today everything went perfect. There were a lot of competitors - that's why the race was so interesting. During the TT I had no radio, so it was impossible to modulate the effort. I only tried to find my tempo, a right pace and I maintained it until the end. "Sylvain was second - as a team we cannot complain about our result today.
"We were one of the best teams for the entire season. I'm proud to be part of this group. Now I will go home, I will reach my family and I will take a period of rest. I think everybody in the peloton deserves it."
The Chrono des Nations is a one-day time trial in the Vendee region of France.