Sustained high-intensity development of society and economy have leading to the degradation and destruction of the wetland in Haihe River Basin. Limited by funds, the wetland protected areas should be selected in cost-effective ways. Previous studies attempted to identify priority areas of wetland protection with only biodiversity features. As a result, the protection targets of many reserves overlap, and gaps still exist of the region. Applied with the methodology of Systematic Conservation Planning and the relevant spatial optimization software, we tried to identify wetland areas in need of protection that were more representatively and effectively, and the conservation gaps based on the existing wetland reserves. Two level of conservation objectives were used in this study, we first established a wetland classification scheme of climatic-geomorphological-wetland, which was employed as a coarse-filter for surrogates of wetland biodiversity, 24 types were derived of the region, we also use water birds as fine-filter as a complementary, the costs for protection were considered with the factors of socio-economical, such as road, rail, etc. Currently, the coastal wetland were protected with the highest percentage of 13.03%, after the optimization, it could reach to 53.14%. Palustrine wetland was the most widely distributed, but only 2.72% were protected, it could be 36.35% with our planning. Compared with the wetland protected areas of the region, only the Tuhaimajia river has been well protected, significant gaps were in other catchments. Lacustrine wetland and palustrine wetland gaps were mainly distributed in upstream of Luan river and Yongding river, riverine wetland gaps were in the border of Tangshan and Qinhuangdao. The source of river were main gap areas, and the outside areas of the reserves also presented a significance of protection, such as the Binzhouhaian Wetland Nature Reserve and Yellow River Delta Wetland National Nature Reserve. In consideration of the prominent influences of Xiongan New Area in the future economic development of the region of Beijing, Tianjin and Hebei, our suggestions were as follows:small-reserves were suggested to established in key rivers of Luan River and coastal areas of Hebei; wetland parks were recommended in the northern Haihe river in face of the dense population and advanced economies; the reserves in the southern Haihe river and Tuhaimajia river should be enlarged and managed more efficiently, as it was the core areas for wetland protection. Our results could be served as reference for the adjustment of wetland protection system in Haihe River Basin, and be useful enlightenment for the integration and optimization of wetland and non-wetland ecosystem.