Climate change is expected to cause more severe warming in temperate regions. In recent years, an extensive amount of researches has been focused on the impact of climatic change on the wetlands. Climate change would affect the hydrology of wetlands mostly through changes in hydrology, direct and indirect effects of changes in temperatures and more extreme floods and droughts. In response, the wetlands would shrink and shift, and followed by reduction and loss of ecological functions. Meanwhile, non-climate factors have increasingly important impacts on the wetlands. Direct impacts included wetland reclamation, overgrazing and drainage. Indirect impacts included building of large-scale water projects and groundwater overdraft. Those would not only led to greater water loss from the wetlands, but also reduced the water inputs from their catchments. Climate changes would make future efforts to restore and manage wetlands more complex. As the main distribution area of freshwater marshes in China, the Sanjiang Plain has undergone fast warming over the past six decades. It is of importance to quantitatively quantify the influence of climate changes on the wetlands. In this paper, the habitat distribution models (HDMs) were used to investigate how and to what extent did climate changes influence wetlands in the Sanjiang Plain. The results showed that over the last sixty years, the Sanjiang Plain has got warmer and slightly drier over the last sixty years and became more suitable for the wetlands. During the period from 1950 to 1980, climate change indicated a positive feedback effect rate of 5.21%, and that in the period from 1981 to 2010 was 4.33%. During the period from 1951 to 2010,non-climate factors were not only the major cause of loss and degradation of the marshes, but also the main obstacles to new marshes forming.