We used the Sanjiang Plain where swamp changes have been more drastic as the research area. Regional differentiation and factors influencing the changes of in swamps in the Sanjiang Plain from 1954 to 2015 at the watershed scale were analyzed using the dynamic degree, landscape index, and Geodetector model, and by combining GIS and RS techniques. The results showed that from 1954 to 2015, the area of swamps in the Sanjiang Plain had a decreasing trend, in which, the loss of wetland area in the Naoli River and Tongfu Basins was the greatest, whereas in the Anbang River, Luobei River, and Weiken River Basins the loss was faster. The variation characteristics of the swamps pattern in each basin within the Sanjiang Plain had some differences. The concentration of patches in the swamps in the Weiken River Basin gradually increased and the degree of fragmentation gradually decreased, whereas the concentration of swamps in other basins gradually decreased and their degrees of fragmentation increased, and the connectivity and stability of swamp patches in all sub-basins showed a decreasing trend, in which, the Anbang River Basin showed the largest decline. The index that best demonstrated the change in the swamp landscape pattern in each sub-basin of the Sanjiang Plain was patch density. Human disturbance was the main factor affecting the changes in swamps in each sub-basin of the Sanjiang Plain. Among the natural factors, the most influence factors on the change of swamps were topography, followed by temperature and precipitation.