Sanjiang plain is the largest distribution area of fresh water swamp in China. The large-scale agricultural activities resulted in a sharp decrease in wetland area, which led to degradation of wetland ecosystem services and a series of ecological and environmental problems. Wetland restoration is urgently needed. The historical biodiversity distribution and landscape structure of wetlands have an important guiding significance for wetland restoration. Based on the analysis of landscape pattern changes of wetlands, we combined conservation value of historical biodiversity (representing restoration value) and landscape structure of wetland (area proportion) to prioritize the wetland restoration efforts. Our results showed that during 1995 and 2015, the total area of Sanjiang plain wetland was reduced from 14308.55 km² to 8532.29 km², and approximately 40% of the original wetland had been degraded into grassland or converted to farmland. Meanwhile, the number of patches has doubled, with the rate of 110.3 patches per year; the patch density increased from 0.15/km² in 1995 to 0.52/km²; the maximum patch area decreased from 21.20km² to 14.64 km². All these figures show that the Sanjiang plain wetlands present overall fragmentation characteristics. The spatial distribution of wetlands in Sanjiang plain is uneven, and the proportion of wetlands in each eastern county is higher, more than 10%; however, the proportion of wetlands in the central and western counties is lower, and the proportion of wetlands in Qitaihe and Youyi county is even less than 5%. Irreplaceability index (IRR) was divided into five grades:0 ≤ IRR ≤ 0.09 (Rank 1), 0.09