Green economy is the inevitable requirement for cooperation between Fujian and Taiwan, but there are many problems such that the green industry system is not complete which is lack of professional talents and independent brands and so on. The significance of solving such problems is to achieve industrial upgrading and structural optimization of the current economy between Fujian and Taiwan. The existing research on development of green economic cooperation between Fujian and Taiwan has not formed mature unified paradigm, most of theoretical results just embodies some discussion papers and policy documents. In this research, we innovatively analysis economic cooperation strategy selection based on Cooperate Game model, then put forward the idea that is to build the Green Economic Zone of Taiwan Strait which has not been proposed before. It is constructive for green industries and green-city cooperating measures to improve economic cooperation between Fujian and Taiwan coupling. The building method may be including policy, city, technology and industry cooperation.