Wetland ecosystems have comprehensive ecological functions and are sensitive to climate change. Under climate change, wetlands plant community productivity and diversity may be affected. In previous studies of wetlands, the effects of climate change have been primarily investigated using field observations, factor-controlled experiments, and mechanism analyses. However, the ecological risks to wetland communities under potential long-term climate change on a regional scale remain uncertain. The Sanjiang Plain is the largest area of natural marsh wetlands and the national ecological functions in China. In this study, the changes in plant productivity and diversity of wetland ecosystems in the Sanjiang Plain were simulated under different climate change scenarios (i.e., Representative Concentration Pathways, RCP 2.6, RCP4.5, RCP6.0, and RCP8.5), and the rank of spatiotemporal risk on a regional scale was estimated using a pressure-state-response model. Temperature and precipitation had average rates of increase of 0.44°C/10a and 12.13mm/10a, respectively, under different climate change scenarios to 2050. The fluctuation range in climatic factors was largest under the RCP8.5 scenario. On a long-term scale, compared with the base year of 2010, vegetation productivity increased significantly under the RCP2.6 scenario, remained almost constant under RCP4.5 and RCP6.0 scenarios, and decreased under the RCP8.5 scenario. In contrast to productivity, plant diversity increased under all four scenarios, but the range of increase gradually decreased with the increase in scenarios. Spatially, a fluctuation range change in precipitation was one of the important factors that caused high risks to regional wetlands. In the northwest of the Sanjiang Plain, most wetlands were assessed as high risk at level-3. In the other regions, the risks were lower with the values below level-2, and only a few places were assessed at risk level-3. In national wetland nature reserves, the northeast of the Qixing River, Xingkai Lake, and the Dongfanghong Marsh wetland area were ranked as high risk at level-3. These findings suggest that wetland protection and management should be focus on hydrological allocation and the potential ecological risks to national wetland nature reserves. However, a joint risk assessment of climate change and human activity should be conducted to provide a comprehensive reference for the protection and development of natural marsh wetlands.