As the country with the world’s largest fishing capacity, China suffers from the depletion of living marine resources, mainly caused by overexploitation, the effects of which also distinctly influence global sustainable utilization of marine resources and maritime order. The country has implemented a series of measures to control its national fishing capacity, notably since the late 1980s, and strongly expressed its responsibility and commitment to sustainable resource utilization in the 13th Five-Year Plan (2016–2020). This study quantitatively assesses the effect of China’s fishing capacity management efforts by examining changes in the fishing capacity of marine capture fisheries by region from 1979 to 2019 in Chinese waters, based on window data envelopment analysis (DEA), and further proposes directions for policy adjustment. The results suggest that China’s coastal and offshore fisheries are still subject to overcapacity of approximately 20%, despite major corrective efforts invested in past decades. This implies that China needs to further improve its fishing capacity management and set clear objectives, as determined by the availability of resources and regional features. Global fisheries management’s focus is shifting from input to output control, but overcapacity still threatens the sustainable use of fisheries resources in China and poses obstacles to other systems.