Object: To Provide a basis for the government optimizing the allocation of health resources. Methods: The overall fairness was analyzed by Theil index and Gini coefficient. The main causes of unfairness were estimated by the decomposability of Thiel index. Results: Health resources owned by the “One-hour Economic Circle” were 1.5 - 2 times than that of the “Two wings”. Theil index and Gini coefficient of five health resources from small to large were sickbed, doctor, health worker, nurse, and medical equipment. Differences within region in the contribution rate of the total Theil index were greater than the difference between region and the tendency to expand. Conclusions: The total amount of the health resources in Chongqing is insufficient. The configuration of doctor is more equitable than nurse, while the medical equipment’ fairness is worst. Differences within region mainly cause the unfairness.