The notion of higher education as an industry is not only a new structure of higher education for Taiwan and Mainland China in the New Economic Era, but also a new interpretation of school management, operation, and rules of competition that have come into being after the entrance of the two nations into the WTO. This study incorporates content analysis and comparative research by describing, defining, and comparing seven performance indexes of the higher education industry for Taiwan and Mainland China. These indexes are: the role of the government, the role of higher education in production in production of goods, the upstream and downstream supply chain effects of educational institutions, institutional structure, competition strategy, chance, demand, and cross-strait exchanges and interaction. Through extensive analysis of the data, this study drafts out four mutual prosperity strategies (MPS) to accelerate collaborative relations cross the strait in the New Economy Era: the digital MPS, the service MPS, the industrial MPS, and the common ideology MPS.