A national nature reserve information management system has been developed based on GIS in order to improve its comprehensive management and service level, and to further integrate and develop information resources. Experiments and demonstration research were conducted in Xiaowutai Mountain National Nature Reserve. The results show that the system including three layers of structure system, four databases, eight major functional modules and six basic functions is able to meet management needs of the reserve. The system achieves multi-source heterogeneous data fusion and comprehensive integration, and promotes business collaboration and data sharing. It combines qualitative analysis, quantitative calculation with visual display to achieve space integrated management mode of information resources in the reserve. The system can provide a reference for information management of national nature reserves in China.