China implemented the National Wetland Conservation Program (NWCP) from 2002 to protect and rehabilitate wetlands. Under the background of sustainable development, assessment on the effectiveness of the NWCP is important to ecosystem management, especially in the Sanjiang Plain, the largest marsh distribution area and hotspot area with wetland loss. To achieve this aim, this study examined the changes in land cover and ecosystem services (ESs) from 1990 to 2000 and from 2000 to 2015 in the Sanjiang Plain as well as the nine national nature reserves for wetlands (NNRWs) by means of Landsat series images and the InVEST model. Results reveal that the NWCP played critical roles in reducing wetland loss and improving regional ESs. The shrinkage rate of wetlands in the Sanjiang Plain has been decreased remarkably, with a declined rate of wetland loss from 750 km(2) yr(-1) to 189 km(2) yr(-1). The reduction rate of habitat area in good suitable grade and ecosystem carbon stock declined notably during the period 2000-2015 compared to the period 1990-2000. The amount of water retention increased by 5.4%, while the grain production capacity was enhanced by nine times from 1990 to 2015. Specifically, since 2000, the reduction rate of wetland area in NNRWs (33 km(2) yr(-1)) was obviously lower than that in the entire Sanjiang Plain, whilst various ESs in NNRWs were better than that in the whole Sanjiang Plain. This study is expected to provide an example for evaluating the effectiveness of the NWCP at other regions and support regional wetland conservation management.