In recent years, Shanghai is exploring the implementation of comprehensive budget management in community health center, but facing some problems in process: the budget management model is still not unified, “separation between revenue and expenditure” policy is not really implemented, the financial subsidies is not combined with performance appraisal. Meanwhile within the center, the personnel funds are approved by public sector, the operation funds are not standardized, and project funds are relatively chaotic. It is recommended to carry out cost accounting of community health center to clarify expenditure, introduce standardized workload in community health center to promote budgeting scientifically, strengthen the information construction to make budget implementation assessment, and establish a performance appraisal linked to the government subsidy mechanism.