Marine fishing vessels are now under localized management, but their offshore production has the characteristics of operating in waters under cross-regional jurisdiction. Traditionally, local fishing vessels generally have significant local characteristics because they follow local fishing experience and traditional fishing habits in inshore waters. However, with the steelization and large-scale of fishing vessels, the operating space of marine fishing continues to expand, so to understand and grasp whether the current marine fishing has regional characteristics differences, it has indispensable scientific and theoretical guiding significance for fishery sampling statistical survey and accurate fishery management. In this paper, the double-towing fishing vessels in Zhejiang, a major marine fishery province, are selected as the research object. Through a large sample random sampling survey, the annual production data of double-towing fishing vessels in three prefecture-level regions of Zhejiang Province are obtained, and the regional differences of fishing capacity (CPUE, catch per unit of effort) and catch structure are analyzed. The results show that except for September, there are significant regional differences in fishing capacity among the three regions, and Ningbo is relatively close to Taizhou, and there are significant differences in catch structure among the three regions in the whole year. Taizhou area is relatively independent and has its own category, while the similarity between Ningbo and Zhoushan is relatively high. Considering the interaction between fishing capacity and catch structure, the difference among the three regions is more significant. Although the production activities of China’s marine fishing vessels are wider and more flexible than those of 40 years ago, the differences in regional characteristics of fishing operations are still obvious, indicating that China’s marine fishery management should be more accurate. in order to continuously improve the level of spatial scientific management of marine fisheries in China.