Based on the theories and methods of landscape ecology and protection biology, “3S” technique and mathematical models were used to plan the wetland biodiversity conservation in the Sanjiang plain. Wetland bird richness and disturbance degree were assessed and calculated by using GAP Analysis. Bird species movement resistance surface was builded and security patterns was judged using species movement resistance model. Landscape elements were identified based on species movement resistance surface, such as strategic points, radiation routes, inter-source linkage, and so on. Some protecting countermeasures were put forward for biological conservation, including extending protecting area, establishing corridors protected area and hotspot, and identifying micro-scale protected area. In conclusion, the study put forward scientific evidence for the protection and management of wetland biodiversity in Sanjiang Plain, and developped and enriched the theories and methods of Chinese biodiversity protection.