Climate change affects the spatial distribution and ecological functions of wetlands by altering the hydrological processes, soil temperature, biogeochemical cycles, and vegetation conditions. The continuous high temperature and drought, as well as other extreme weather conditions, have led to the degradation of habitats of some urban wetlands, posing a serious threat to the safety of urban biodiversity. The increasingly rapid urbanization is exacerbating wetland fragmentation and reducing the hydrological connectivity of wetlands, and thereby increasing the fragility of wetland ecosystems and leading to the degradation of wetland habitats. Establishing a continuous wetland ecological protection network system is beneficial for mitigating the negative impacts of climate change and urban development and improving biodiversity conservation. The current spatial distribution of wetlands in Beijing is characterized by small patch size and high fragmentation. Despite facing numerous challenges such as water scarcity and fragile water environment, Beijing aims to increase the area of wetlands and promote efforts related to wetland protection and restoration. To optimize the priority conservation pattern of wetlands and address the impacts of climate change and urban development on wetland biodiversity in Beijing, this study adopts the approach of Systematic Conservation Planning which can resolve the conflict between biodiversity conservation and urban resource utilization based on the simulated annealing algorithm. In order to provide more scientific evidence and suggestions for the protection of biodiversity in Beijing, the Marxan spatial optimization model is used in combination with the PLUS and MaxEnt models to simulate and predict the priority areas for wetland protection in Beijing, identify protection gaps, and establish a classification system for wetland protected areas. The result showed that there was a protection gap of 80.15 km² of Beijing's wetlands in 2020. After optimization, the proportion of protected wetland areas will be 87.54% in 2035 and 85.95% in 2050. Under the premise of satisfying the predetermined biodiversity conservation objectives, the result complies with the wetland conservation rate requirements outlined in the wetland conservation planning of Beijing. To optimize resource allocation, the study considers the impact of temporal and spatial changes on the spatial distribution of wetland protected areas and proposes a classification system comprising permanent wetland protected areas, the first-level temporary protected areas, and the second-level temporary protected areas. And the result showed that by 2050, their areas would reach to 488.61 km², 13.02 km² and 28.95 km² respectively. This provides a basis for the phased construction of wetland protected areas, optimization of the wetland ecological protection network system, and conservation of wetland biodiversity in Beijing.