Abstract: The Bohai Sea and the Yellow Sea have been the essential marine granary and eco-environmental governance areas in China. Wherein the carbon dioxide emission from fishing vessels can be normally neglected to assess the global greenhouse gas (GHG). It is very necessary to identify the specific contribution of the productive fishing vessels to the GHG emission, in order to reduce the carbon emission for the carbon neutral. Taking the Bohai Sea and the Yellow Sea as the research areas, this study aims to explore the spatiotemporal characteristics of carbon dioxide emission from the fishing vessels. A dynamic calculation model of carbon dioxide emission from fishing vessels was established using vessel management and position data, in order to reveal the impact of fishery production activities on climate warming. Nine types of fishing vessels were also selected to analyze the carbon dioxide emissions intensity and spatiotemporal characteristics from 2020 to 2021. Results showed that: 1) The total carbon dioxide emissions of fishing vessels in Bohai Sea and the Yellow Sea were 4.5 and 9.45 million tons, respectively, indicating the distribution characteristics of low nearshore and high offshore. Hot spots were distributed mainly in the fishing ground of Bohai Bay, Luanhekou, Haidong, Yanwei, Shidao, Shidong, Haizhou Bay, and Daisha. Every ton of fishing catches emitted approximately 1.57 and 3.27 t of carbon dioxide, respectively, when considering the yield data. 2) Trawler and gillnet fishing vessels were the main contributors to the total carbon dioxide emissions, accounting for more than 70% of the total emissions from all fishing vessels. Among them, the auxiliary vessels were the highest, followed by the purse seiner vessels, in terms of emissions per vessel per unit sailing time. Carbon dioxide emissions per unit sailing time from the single vessel were similar to the trawler, gillnet, stow net, purse seine, auxiliary, and unknown types, whereas, there was the significant difference for the line, and aquaculture types. 3) There was the similar spatial distribution of carbon dioxide emissions from the fishing vessels in the same month in the different years. But the hot spots exhibited a strong spatial difference. Firstly, the hot spots occurred in the central and southern part of the Yellow Sea from January to April, where a high-value belt was extended the southeast from the Haizhou Bay to the East China Sea. Then, there was no carbon dioxide emission in the offshore area from May to August. Eventually, the hot spots were shifted to the central Bohai Sea, the eastern Shandong Peninsula, and the central Yellow Sea from September to December. In general, the center of gravity of carbon dioxide emission from the fishing vessels was transferred from the coastal to the central open waters. The finding can provide a theoretical basis for the transformation of fisheries into the low carbon. Two suggestions were also proposed to reduce the carbon emissions of fishing vessels. One is to accelerate the transformation of fishery production and product formats, and another is to strengthen the carbon emission management of key fishing vessels and key areas. In the end, it can be expected to assess the carbon emission system for the fishing vessels.