Shapotou National Nature Reserve is one of the earliest desert ecosystem reserves in China, which is located in northwest part of Ningxia Autonomous Region. Many different bird species have been recorded in the desert, wetlands, fixing sand forests, and the villages within this reserve. However, with the development of desert tourism and the West-to-East Gas Project, the distribution and constituents of the land-use has changed, which has affected ecosystem services. A major threat faced by many birds that needs to be addressed urgently is habitat loss, degradation, and fragmentation. It is obvious that with increased awareness of the importance of protecting biodiversity, the demands for addressing ecological security becomes an urgent need. Given this background, in this study, we aimed to identify significant bird habitats and their spatial distributional patterns, data that is of vital importance for informed conservation action for birds. This study applies Security Pattern Theory to identify landscape area or elements of critical significance to safeguard bird activity. We chose Shapotou National Nature Reserve as the study region for three reasons. (1) This reserve has a high percentage of rare bird species, and hence the results would have good representativeness; (2) Although the total area of this nature reserve is just 140.43 km², the habitats are becoming highly degraded and fragmented; (3) With the advent of human activity in the reserve, comprehensive planning for protection becomes very important. Our results show the following:(1) it is feasible to construct a landscape security pattern, based on GIS and "cost distance" analytical tool, and using environmental factors and human interference factors in the minimum cumulative resistance (MCR) model. This also provides a feasible approach to construct ecological security pattern for particular species in other nature reserve. (2) Through the minimum cumulative resistances surface, which was derived from the MCR model, we identified the components of ecological security pattern such as corridors, radiating routes, strategic points, etc, which can preserve or positively affect bird populations. (3) This security pattern addresses the environmental and economic scenario at Shapotou National Nature Reserve well. Based on this model output, the identified "source" habitats for the birds were concentrated, resulting in relatively low fragmentation, and allowing more effective and easily implementable actions for their protection. To connect the "sources" 13 corridors as well as 85 radiating routes were identified, which provide more space for "sources" expansion. Additionally, we identify the weakest position of bird activity as the strategic point combined with key regions to protect the whole structure of the bird's activity. Our results provide an effective method to protect particular species within this nature reserve. Further studies will be valuable as more factors could be identified by the ecological security pattern, and the correlation between the various factors was not significantly reflected in this study.