Object: To evaluate the effect of inpatient cost under the background of the capitation payment reform in new rural cooperative medical system (NCMS). Methods: We performed retrospective time series analysis of the inpatient cost in NCMS fund by analyzing monthly data in Pudong New Area from the year of 2011 to the year of 2015. Results: In 40 months after the policy intervention, the mean insured inpatient cost per visit (RMB 11176.95) was increased by 34.99% than 20 months before (RMB 8279.66). The mean forecasted inpatient cost per visit (RMB 12836.63) was higher than observed values ( P<0.001). And it was statistically the same between the observed and forecasted number of inpatients of the corresponding period by simple seasonal model (P>0.05). Conclusion: In over 3 years after the policy intervention in NCMS, it was effective in cost curb of expenses excessive growth for inpatients, and d id not inhibit the normal release of their medical service demand.