With the intensification of human activities, production, economic development and other activities, wetland area is shrinking, wetland fragmentation is becoming popular, and a large number of isolated wetlands are accordingly formed. Based on pressure-state-response theory and analytic hierarchy process (AHP), a wetland conservation priority model was constructed to evaluate the marshes in the Sanjiang Plain. The results showed that: 1) The spatial distribution of natural wetland conservation priority in the Sanjiang Plain shifted from a pattern of high-in-northeast and low-in-southwest to that of high-in-east and low-in-west from 2000 to 2020, while the isolated marshes changed from a pattern of high-in-northeast and low-in-southwest to that of dispersed and irregularly spatial distribution; 2) The conservation priorities of natural marshes and isolated marshes have moved from northeast to southwest, and the conservation priority intensity of isolated marshes and non-isolated marshes in Sanjiang Plain showed a decreasing trend from 2000 to 2020. The reduction magnitudes of isolated marsh was larger in 2020 than that in 2000; 3) The protection priority of isolated marshes outside the protected area was higher than that of isolated marshes inside the protected area; 4) The driving force and conservation priority of isolated marsh, the protection strategy of isolated marshes in the Sanjiang Plain was then proposed based on the evaluation results The strategy includes two aspects: one is to place priority to the protection of the existing important isolated swamp wetland, and to restore the lost important isolated swamp wetland; and other is to strengthen the protection of isolated marshes outside the protected area, especially the protection of the isolated marshes within the 6 km buffer zone outside the protected areas.