Biodiversity conservation plays an important role in maintaining the function of urban ecosystem. In this study, 39 species of key protected plants in Xiamen were selected as the objects. MaxENT, a species distribution model is used to predicate the potential distribution of species. Zonation, a quantitative tool for Spatial Conservation Priority, is used to identify the areas that are suitable for the survival of key protected plants and can ensure the landscape connectivity, so as to obtain the multi species landscape protection level of local key protected plants. According to the 2020 global biodiversity target, 17% of the areas with the highest level of landscape protection will be regarded as the spatial conservation prioritization areas of multi species. Combined with the weighted extinction risk curve with landscape loss generated by zonation model, 8% of the areas with the highest level of protection are classified as primary conservation areas, and the areas with the protection level ranging from 8% to 17% are classified as secondary conservation areas. By using jackknife method in MaxENT, it is found that altitude is the most important environmental factor affecting the distribution of local key protected plants, and spatial conservation prioritization areas are concentrated in the coastal zone with lower altitude. The spatial conservation prioritization areas in this study were compared with nature reserve, the planning of ecological function zones, land use planning and urban master planning of Xiamen, it is found that the spatial conservation prioritization areas in the West and north of Xiamen are well protected; the spatial conservation prioritization areas in the coastal zone of southwest and southeast of the island and the eastern and southern of outside the Xiamen island have been occupied by construction land on a large scale. there are few areas included in the scope of nature reserves, and a large number of coastal conservation prioritization areas are vacant; although the part of the conservation prioritization areas in the southeast of outside the Xiamen island are not occupied, they are planned as reserve land for development and lack of ecological protection. In order to avoid the further reduction of conservation prioritization areas, we should focus on the ecological protection of conservation prioritization areas in the coastal zone. The conservation prioritization areas that belong to development reserve will be converted into ecological space. We should strictly control the further development and utilization of conservation prioritization areas in the coastal zone so as to protect biodiversity. For the primary and secondary conservation areas, we should implement rigid and flexible ecological conservation measures, and coordinate the relationship between protection and development in conservation prioritization areas.