By constructing the decision tree model, the main wetland types such as swamp meadow wetland, swamp wetland and lake in Heihe River and Baihe River basins was divided. Three landscape pattern indices were selected to analyze the change characteristics of wetland types, and the driving factors of wetland change were analyzed by principal component analysis. The results show that the total area of wetlands in Heihe River and Baihe River basins has increased since 2000, and the change trend of swamp wetlands is opposite to that of meadow wetlands. The regional differences of wetland changes in the two river basins are significant. In the Heihe River Basin, the area of meadow wetland increases with the reduction of the fragmentation degree. And the area of swamp wetland decreases with the patch density reducing, and there is local contiguity. In Baihe River Basin, the area of swamp wetland increases. Under suitable topographic and hydrological conditions, meadow wetland and surrounding meadow can be transformed into swamp wetland. The wetland change in the two river basins has the interactive characteristics of “socio-economic+agricultural and animal husbandry factors+climate change”, and socio-economic factors play a leading role in the interdecadal scale wetland change.