Ecological security is an important cornerstone of the national security system. Nature reserves are important safety barriers to maintain regional biodiversity, which play an important role in water conservation and ecological balance, and can effectively alleviate the damage of social development to the natural environment. Jiuzhaigou National Nature Reserve is located in a sensitive area, the ecological security status of the Jiuzhaigou Nature Reserve under the impact of natural disasters and human activities has attracted much attention. On the basis of comprehension and analysis of eco-security, 23 assessment indexes were selected by the Pressure-State-Response (PSR) model and obstacle factors analysis from the aspects of natural environment, human activities and social economy to evaluate the ecological security status of Jiuzhaigou National Nature Reserve and identify the main obstacle index of Jiuzhaigou from 2001 to 2019. The results show that (1) the level of ecological security in Jiuzhaigou National Nature Reserve has been gradually improved from 2001 to 2019, with the index increasing from 0.7933 to 0.8623. Among them, the pressure and state index indicated a downward trend of fluctuations, and the response index presented an upward trend. (2) In general, Jiuzhaigou National Nature Reserve was in a safety state, and only a few years were affected by geological disasters and fell to the critical safety level. The evolution of the safety level is in the order of safety, critically safety, safety, critically safety and safety. (3) In criteria layer, the main obstacle of the ecological security came from the pressure layer, and the main obstacle index were the annual growth rate of residents in nature reserve (C2), the frequency of geological disasters (C6) and the degree of legal revision (C22), with the degree of obstacles 12.63%, 10.53% and 9.47%, respectively. (4) With the improvement of disaster prevention and management system, the main obstacle factors changed from the degree of legal revision (C22), the degree of sewage treatment (C20) and the degree of geological disaster prevention (C17) to the frequency of geological disasters (C6) and the annual growth rate of residents in nature reserve (C2). To improve the ecological security, the environmental investment should be increased, environmental protection intensified, prevention of natural disasters improved. At the same time, measures should be taken to optimize the system of community co-management, explore the scientific path for harmonious and sustainable development of natural protection and community residents, and steadily improve the level of ecological safety of Jiuzhaigou National Nature Reserve.