Objective: To study the influence route of medical separation policy on the quality of hospital economic operation by using medical expenses as an intermediary variable. Methods: regression analysis and intermediary effect test were used to verify the relationship between the policy of separating medicine and the quality of hospital economic operation ,the intermediary role of medical expenditure. Results: the drug income and hospital service income, financial subsidy income were positively correlated with the quality of economic operation and hospital medical expenses, medical expenses plays an intermediary role in the total income of drug income and hospital, in the hospital financial subsidy income and asset liability ratio play an intermediary role between, the mediating effect of financial subsidy income and total income in the hospital between. Conclusion: the medical separation policy indirectly affects the hospital revenue through medical expenses. Reasonable adjustment of medical service price, straightening out the medical expenditure structure and increasing financial input are the key links to change the policy of separating medicine from the total income of the hospital