Objective: To explore a measuring method of balancing the funds of Basic Medical Insurance System for Urban and Rural Residents and to provide scientific suggestions for social medical insurance management departments and related researchers. Methods: Through the cross-sectional investigation to obtain parameters of the insured population, Monte Carlo simulation model was constructed to estimate the fund balance based on kinds of reimbursement schemes. Results: The insured population hospitalization rate was 8.76% in 2014, the proportion of hospitalization within the county was 40%, and the actual reimbursement ratio was 52%. The township hospitals, county hospitals, municipal hospitals and outside Wenzhou hospitals actual reimbursement ratio were increased to 82%, 75%, 56% and 51% respectively, the fund utilization ratio were 91%, 95%, 99% and 96% respectively. Conclusion: When the reimbursement ratio of the county hospitals and municipal hospitals was improved, the fund utilization ratio was relatively high. This study proposed reimbursement policy continues to focus on the primary health institutions. Stochastic simulation technique can provide a new method for medical insurance fund balance calculation.