Ma ran unopposed in today's balloting. Some 380,000 Nationalist members were eligible to vote.
Ma is scheduled to complete his second presidential term in May 2016. Term limits prevent him from running again.
Ma's re-election as Nationalist Party head prevents any of his would-be successors in the Nationalist ranks from getting a leg up in the 2016 presidential race.
Premier Jiang Yi-huah, Vice President Wu Den-yih, Taipei Mayor Hau Lung-pin and Xinbei City Mayor Eric Chu have all been mentioned as potential presidential candidates for the Nationalists.