Objective: The economic operation of target provincial budget medical institutions during the "13th Five-Year Plan" period was analyzed to provide basis for government decision-making during the "14th Five-year Plan" period. Methods: Descriptive analysis and comparative analysis were conducted on the economic operation of target provincial budget medical institutions through the income, expenditure and economic operation indicators of medical institutions based on the financial annual report data from 2016 to 2020. Results: In 2020, the proportion of fiscal subsidy income and basic expenditure subsidy in total expenditure of target provincial budget medical institutions were 21.96% and 8.28% respectively, the proportion of drug expenditure was reduced to 26.40%, and the proportion of health material expenditure, public expenditure and administrative expenditure were 15.51%, 4.19% and 15.51% respectively. The annual per capita salary of employees on the job was 134600 yuan, the asset-liability ratio was 58.38%, the current ratio was 1.18. The turnover of total assets, current assets and fixed assets were 51.12%,114.63% and 161.22% respectively. The net value of fixed assets was only 55.61%. The ratio of pharmaceutical income to medical income was 33.35%, and the utilization rate of hospital beds had dropped to 44.49%. Conclusion: The proportion of financial subsidy of target provincial budget medical institutions needs to be improved, the low debt paying ability needs to be strengthened, the economic operation efficiency needs to be improved, and the fine management needs to be strengthened.