The wetland biodiversity had been severely disturbed and destroyed due to the global climate change, land reclamation and exploitation activities. Wetland biodiversity conservation was increasingly concerned for its functions and service values those have been recognized and accepted widely. The key issues about wetland biodiversity conservation concerning were to how the wetland biodiversity spatial pattern to distribute and where hotspots to identified. The spatial pattern of wetland bird diversity was analyzed by using the spatial autocorrelation model with the combination of forecasting the wetland bird distribution provided by GAP analysis. The hotspots and superior conservation order of bird diversity were identified by using GIS technology. The study results indicated that the high-high wetland bird richness focusing field was the best place for build or enlarge nature reserves where main distributed around protected areas and coastal rivers, the high-low wetland bird richness focusing field was the best place for build micro-scale protected area where mainly in the agricultural landscape. 13 hotspots were identified by using the indicators as followings: wetland bird richness, nationally protected birds, habitat types and structural, the closest distance from hotspot to nature reserve, fragmentation, disturbances, etc. The total area of hotspots was 1018.7 km², accounting for 8% of the total research area. 13 hotspots were divided into three kinds of superior conservation order of biodiversity using by system cluster analysis. In conclusion, the study put forward to scientific evidence for the protection and management of wetland biodiversity in Sanjiang Plain, and developed and enriched the theories and methods of Chinese biodiversity protection.