Objective: To analyze the status and differences of health resources allocation in undeveloped areas of Chongqing, China, and to provide empirical evidence for health planning and further optimization of health resources allocation. Methods: The comprehensive evaluation system for health resources allocation in underdeveloped areas was constructed. Afterwards, the entropy weight TOPSIS method was used to comprehensively evaluate the level of health resources allocation in 22 underdeveloped areas of Chongqing, and the K-means cluster analysis method was used to classify the comprehensive evaluation results. Results: The level of health resources allocation in Chongqing’s underdeveloped areas was relatively low and the regional differences were significant. The level of health resources allocation in 22 underdeveloped areas can be divided into 4 categories, of which Shizhu, Nanchuan, Qianjiang, and Liangping were better, Wuxi, Hechuan, Tongnan, and Youyang were poorer. Conclusion: It is recommended to increase the differentiation and pertinence of health policies in undeveloped areas, to achieve dynamic management and control of health resources, to promote the sustainable development of human resources for health, and to ensure that the level of health financing is improved.