Abstract: China’s marine economy has developed rapidly and became the new growth point of national economy. At the same time, the regional marine production capacity in China shows a significant regional heterogeneity. Based on construction of input and output evaluation system of fishery economy, and applying the combination of panel data and quantile regression, variable coefficient regression methods, this paper analyzes the regional heterogeneity of the input and output of coastal fishery economy in China. Empirical results show that fishing boats and other capital inputs contribute significantly to the economic development in China fishery industry. However, fishery workers, the size of aquaculture area of fisheries play limited roles in China coastal fishery economy. Result also indicates that China’s fishery economy is in the stage of increasing returns to scale and science and technology has become an important driving force for the development of fishery economy in China. Coastal fisheries resources in China have not yet reached the optimal allocation status. Fishery development input allocation utilization in Pan Pearl River Delta region is superior to that in Yangtze River Delta and the Bohai region. In general, the fishery economy developments in different regions show significant heterogeneity.