The Sanjiang Plain includes the largest freshwater marsh in China, playing an important role in regional carbon cycle. As an important indicator of carbon cycle, the net primary productivity (NPP) is a crucial index for estimating the carbon storage of marshy wetlands. Investigating the association between climate factors and NPP variation quantitatively is of great significance for estimating carbon sequestration of marsh. Based on NPP data and climatic data from 1954 to 2014, the spatiotemporal change of NPP in marsh area was analyzed and its association with climate factors was investigated in the Sanjiang Plain in this study. The results indicated that the NPP showed an increase trend in the marsh area of the Sanjiang Plain in the past six decades. Temperate growth made the largest contribution to the NPP increase among the main climate factors in the last six decades, followed by CO2concentration. Solar Radiation had the largest explanatory power on the spatial distribution of NPP among three climate factors before 1985. After 1985, temperature played an important role in leading the NPP distribution. Results also showed that the explanatory power of interactions between climate factors was stronger than that of single factor. Our results highlight the asymmetric effects of interactions between climate factors on marsh vegetation, which should be adequately considered in estimating carbon sequestration in marsh area in the Sanjiang Plain.