Abstract: Objective: The study aims to analyze the reasons for operating loss of sample hospital so as to resolve the developing predicament of children’s hospitals. Methods: The study made a thorough analysis on the operation loss from the perspectives of volume of business, incomes structure, cost of medical care, medical treatment project costs, healthcare reform policies etc. by comparing the financial data from 2013 to 2015. Results: According to the analysis results, the operating loss of sample hospital can be attributed to the following reasons. Firstly, the healthcare pricing is underpaid with the high service costs. Secondly, the quantity of outpatient service declines with the change of incomes structure. Last but not least, the financial compensation by legal in not fully funded. Conclusion: From the perspective of external policy, government medical service pricing should reflect the particularity of pediatrics and government should increase the public subsidy to children’s hospital. From the perspective of hospitals, children’s hospital should optimize the service process, develope the characteristics of specialized pediatrics, and take other measures to improve healthcare quality and enhance market competitiveness.