Wetlands are among the most important habitats of highly wetland-dependent waterbirds but are subject to ongoing habitat loss and degradation owing to intensified anthropogenic activities. The scarcity of human and natural resources makes effective habitat protection an important concern. Here, we aimed to investigate waterbird habitat protection methods for Anhui Province, China, a critical stopover and wintering area on the East Asian-Australasian Flyway that features rich wetland resources subject to significant habitat loss and degradation. We evaluated the status and importance of 306 wintering waterbird habitats and identified the key environmental influences and current protection gaps using the entropy weights method and generalized additive modeling. We found 73 important habitats for waterbirds in Anhui Province, which were classified into levels of importance (descending from I to V) according to the natural discontinuity method. Level I and Level II habitats were mainly located in the Yangtze River floodplain and Level IV habitats in the Huaihe River floodplain. The gap analysis showed that 42 important waterbird habitats had protection gaps, accounting for 57.53% of the total area. Waterbird habitat importance was significantly correlated with elevation, normalized vegetation index, lake area, and lake circumference but not with distance from roads or population density. The results of this study provide scientific information for waterbird habitat conservation planning, which is crucial for maintaining wetland ecosystem functions.