Ecological security of natural resource is an important component of national security, and the regionalization of natural resource ecological security provides an essential approach to ensure regional sustainable development. Based on the natural resource data, ecological environment data, and relevant regionalization materials, this article constructs a natural resource ecological security evaluation index system from the perspectives of ecological sensitivity and ecological service importance, then reveals the spatial pattern of China's natural resource ecological security. By establishing the principles and indicators of regionalization, according to the fact that the first-level area mainly reflects the spatial distribution pattern of natural resources, and the second-level area mainly reveals the difference in natural resource ecological security level, the Self-Organizing Feature Map (SOFM) neural network is used to formulate a regionalization scheme for the natural resource ecological security in China. The results show that:(1) The overall level of ecological security of natural resource in China is relatively low, with most of the areas being classified as having moderate to high levels of warning. Only 24.22% of the regions have a safe or relatively safe state. The areas with low-security levels are primarily located in the arid and semi-arid regions west of the 400mm precipitation line. On the other hand, the areas with high-security levels are concentrated in the southeastern parts of the country, where water, heat, and biological resources are relatively abundant. (2) The natural resource ecological security regionalization scheme for China includes 8 first-level zones and 27 second-level zones. We summarize a comprehensive summary and analysis of the unique features and ecological security threats of natural resources in each major region. Moreover, we present practical recommendations to address the challenges faced by natural resources in the secondary regions to enhance their ecological security status. The research results can provide theoretical support and a decision-making basis for promoting the sustainable utilization of natural resources and the optimization of national land space by regionalization and classification.