China, Japan and South Korea have a close relationship in aquatic products trade. Japan and South Korea are both China’s important export markets. Based on the data of UN Comtrade Database from 2001 to 2012, the paper compares the trade status of China’s aquatic products exported to Japan with those exported to South Korea, and then use the CMS model to figure out the factors that influence the volume growth of the aquatic products of China exported to Japan and South Korea. The results show that, the increasing demand of Japan and South Korea is the main factor that promotes the export growth of China’s aquatic products. The product structure effect and the comprehensive competitiveness effect of China’s aquatic products in Japan market are higher than in South Korea, while the product competitiveness effect and cross effect are not obvious in the two markets. Based on the results of empirical research, the corresponding policy recommendations are given.