Abstract: The development of marine fishery economy is an important measure to realize the development strategy of marine power. This paper put forward the index system of comprehensive net performance evaluation of marine fishery from the angle of input and output, constructed the mathematical model of comprehensive net performance evaluation of marine fishery, and analyzed the comprehensive performance of marine fishery in coastal provinces, autonomous regions, and cities in China. The conclusions were as follows: (1) the Comprehensive net performance index system of marine fishery development was more scientific, comprehensive and Realistic than the benefit evaluation that only focused on output; (2) there was a significant north-south difference in the comprehensive net performance of marine fishery in China. The provinces, autonomous regions, and cities with higher comprehensive net performances than the average which are mostly located south of the Yangtze River, and the return rates of the top 5 provinces, autonomous regions, and cities of input and output of marine fishery were generally low; (3) the development of marine fishery in China was still dominated by capital and labor input, and the capital investment ratio was correlated with the level of economic development; (4) the proportion of economic, social, and environmental performance were balanced, and the difference was not obvious between Coastal provinces, cities, and autonomous regions.