With the intensification of climate change, incorporating climate information into protected areas planning has become crucial in reducing biodiversity loss. However, the current natural reserve system in China does not take climate information into account. Therefore, we assessed the effectiveness of existing protected areas through climate refuge and connectivity rankings, and Zonation software was used to identify the ecological priority zone in China by combining climate indicators and human footprint. The results show that the current natural protected areas in China have certain limitations in dealing with climate change, and some protected areas may struggle to maintain their value in biodiversity conservation under climate change. Moreover, China still has lots of important areas that can maintain biodiversity under climate change, but most of them are not covered by protected areas. The results provide support for the planning of China's nature protected area system in response to climate change.