Abstract: Based on "The Technical Guideline on Gross Ecosystem Product(GEP)", this study constructed a general dynamic accounting model for wetland GEP based on departmental surveys, literature statistics, natural and geographical data, etc. The results showed that the average annual GEP of the wetland along Yangtze River in Nanjing was 2.968 billion yuan. Longpao wetland had the highest GEP of 1.088 billion yuan, followed by Xinjizhou wetland and Lvshuiwan Wetland with 0.93 billion yuan and 0.65 billion yuan, respectively. Baguzhou Wetland had the lowest GEP of 0.3 billion yuan. Among the GEP components, the value of climate regulation was the highest, which was 1.511 billion yuan, accounting for 50.89% of the total GEP. The values of flood storage, species conservation and soil conservation were 18.98%, 15.88% and 5.46%, respectively. The value of ecological functions such as water purification, water conservation and scientific research tourism accounted for less than 9%. From the perspective of inter-annual changes, the average annual GEP fluctuated between 1.693 billion and 5.566 billion yuan, and the GEP in different time period was significantly different. Natural factors were an important driving force for the evolution of GEP along Yangtze River in Nanjing, but the impact of social policy factors couldnot be ignored. For example, returning farmland to wetlands would effectively promote the improvement of GEP in local wetlands. In the context of the protection of Yangtze River, the average annual growth rate of GEP in Lvshuiwan wetlands was 24 million yuan. The dynamic accounting results of GEP along Yangtze River in Nanjing would provide a valuable reference for the government to establish a wetland ecological benefit compensation mechanism and carry out the protection of the Yangtze River.