Abstract: Fujian has become an important province in the openingup and cooperation of the Chinese mainland to Taiwan for its geographical advantage, but the services cooperation between Fujian and Taiwan has been behind the cooperation of primary and secondary industries. With the implementation of the strategy of Fujian Free Trade Zone, the services cooperation between Fujian and Taiwan are facing great opportunities. The present situation of the services cooperation between Fujian and Taiwan was analyzed in this paper. Then, the challenges in the services cooperation between Fujian and Taiwan were described, and the opportunities for the services cooperation between Fujian and Taiwan under the strategy of Fujian Free Trade Zone were further analyzed. Finally, the countermeasures were put forward for improving the services cooperation between Fujian and Taiwan according to the existing problems.