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Background At present, the problem of regional imbalance and lack of fairness in the allocation of medical resources in China remains prominent. The report of the 20th National Congress of the Communist Party of China clearly stated that it is necessary to promote the expansion of high-quality medical resources and balanced regional layout. Objective To explore the specific path to improve the efficiency of medical resource allocation in China, and provide scientific reference for realizing the rational and high-efficient allocation of medical resources in China and promoting the equalization of basic public services. Methods The study was conducted from September 2022 to February 2023, and the data were derived from the 2021 China Statistical Yearbook and 2021 China Health Statistics Yearbook. The data envelopment analysis (DEA) method was used to measure the efficiency of medical resource allocation in 31 provinces of China in 2020, considering the number of healthcare institutions, health technicians, and beds as input indicators, the number of visits and admissions as output indicators. Fuzzy-set Qualitative Comparative Analysis (fsQCA) was used to explore the synergistic influence mechanism of internal and external factors on the efficiency of medical resource allocation from a group perspective, taking resource allocation efficiency as the outcome variable, the ratio of health technicians, number of beds per 1 000 population, average hospitalization days of discharged patients, gross domestic product (GDP) per capita, disposable income of the residents, the fiscal revenue decentralization, and ratio of the budgetary expenditures on healthcare as conditional variables, to analyze the conditional configuration of high or non-high level of healthcare resource allocation efficiency, and clarify the multiple paths of efficient and inefficient allocation of medical resources. Results In 2020, the overall level of medical resource allocation efficiency in 31 provinces of China is relatively high, with an average of 0.852, but there were large differences among provinces. The results of configuration analysis showed that the improvement of medical resource allocation efficiency is the result of multiple factors, there are three paths for efficient allocation of medical resources. Path 1: government-led driving path, taking Guangxi Zhuang Autonomous Region as a typical case; Path 2: internal and external coordination driving path, represented by Yunnan Province and Gansu Province; Path 3: balanced driving path, with Guangdong Province, Fujian Province and Hubei Province as representative cases. There are also three paths of non-high medical resource allocation efficiency. Path 1: government-restricted path; Path 2: economic-government dual restriction path, representative cases included Heilongjiang and Jilin Province; Path 3: internal and external constraints path, the typical cases were Shanxi Province and Tibet Autonomous Region. Conclusion The internal and external elements and synergies between elements jointly affect the allocation of medical resources in the process of benign interaction, it is necessary to optimize the internal and external environment, and effectively integrate the key resource elements to form a joint force to promote the rational allocation of regional medical resources.