The new economy era places higher education into a changed and influential position. Successful admission of Taiwan and Mainland China into the World Trade Organization not only intensify, but also change higher education management, operation, and rules of competition in such arena. Education industry will become a main stream of higher education system for Taiwan and Mainland China in the 21th century. Therefore, how to develop friendly relations between Cross-strait and construct the model of cooperation as well as competition will be a critical issue. Considering universities as operating in an education industry, this study incorporates content analysis and comparative research by analyzing, describing, defining, and comparing six performance indices of this industry for Taiwan and Mainland China. These indices include the role of government, production factors at the university level, university upper system, institutional structure and competition strategy, plus opportunity, and demand factors. Though extensive analysis of the data, this study proposes four mutual prosperous strategies (MPS) to promote peaceful relations across the strait: digital MPS, service MPS, industry MPS, and increasing common ideological MPS.