Science and technology innovation is an important driving force to promote the development of fishery industry, and is very important to improve the quality of fishery development. In this study, the Super-SBM model was used to evaluate the fishery science and technology innovation efficiency of 30 provinces and cities in China (excluding Hong Kong, Macao, Taiwan and Tibet) from 2011 to 2020. Combined with the kernel density estimation, the spatial and temporal differentiation characteristics were analyzed. Then, from the two dimensions of investment scale and innovation efficiency, the sustainable development types of fishery science and technology innovation were classified. The results show the following: (1) From the perspective of efficiency change, the overall efficiency of fishery science and technology innovation in China increased first and then decreased during 2011–2020, but the overall efficiency level was low, and the efficiency difference between regions gradually widened, and the eastern coastal regions became the development core of fishery science and technology innovation. (2) From the perspective of spatial differentiation characteristics, there was a large gap between the coastal and inland areas in China. The high-efficiency areas were mainly concentrated in the coastal provinces and cities, such as Guangdong, Jiangsu, Shandong, Shanghai and Tianjin, showing a decreasing trend from east to west. (3) From the perspective of investment scale and innovation efficiency, the study regions can be divided into four types: leading area, breakthrough area, catch-up area and backward area. This paper mainly calculates the efficiency of fishery science and technology innovation in various regions, and divides the type areas of fishery science and technology innovation and development. According to the advantages and problems of different types of areas, different development strategies and correction measures are proposed, which can effectively improve the efficiency of resource utilization, avoid resource waste and realize the sustainable development of fishery.