Beijing freed Chu Kung-hsun and Hsu Chang-kuo, who were held in China for nine years, in exchange for Li Zhihao, who was jailed in Taiwan 16 years ago.
Local media say it is the first time the two sides have swapped spies.
There was no immediate comment from the Chinese government.
"This is based on a mutual goodwill gesture delivered by the Ma-Xi meeting," presidential spokesman Charles Chen said in a statement.
"President Ma (Ying-jeou) hopes cross-strait mutual exchanges can continue and make more concrete achievements in the future," he added.
President Ma has been broadly friendly towards mainland China during his time in office, boosting tourism and trade ties.
Earlier this month, he and Chinese President Xi Jinping met in Singapore - the first time the leaders of China and Taiwan had held talks in more than 60 years.
China views Taiwan as a breakaway province which will one day be reunited with the mainland.
But many Taiwanese see it as independent and are concerned at China`s growing influence.
