The Qianhai Shenzhen-Hong Kong Modern Service Industry Cooperation Zone, as another pilot project of reforming and innovation of Shenzhen Special Economic Zone, will emphasize Shenzhen -Hong Kong regional cooperation. But the cooperation and competition among governments are of public choice, and the development of Qianhai is related to the decisions made or to be made by the Central Government and local governments of Hong Kong, Guangdong and Shenzhen. This study explored and analysed the strategy selection of Qianhai Cooperation Zone by Hong Kong and Shenzhen governments using game theory. We believed that the goal of maximizing local benefits on the part of local governments, as the local interest protectors, will inevitably result in problems such as local protectionism, market segmentation, and synergetic development and so on. More importantly, the coordination by the Central Government is a valid channel shifting from the Prisoner's Dilemma to the Cooperative Game for the development of Qianhai Cooperation Zone, thus providing references for the study on the development strategy of Cooperation Zone.