Objective: To compare cash flow statement between Government Accounting System and Hospital Accounting System, so as to provide some advice for the restructuring of the Cash Flow Statement for Government Department. Methods: the literature method and comparison method were involved. Results: There are four differences between Government Accounting System and Hospital Accounting System, and there are some problems in cash flow statement in Government Accounting System.Conclusion: we restructure the cash flow statement for government department on the basis of Government Accounting System and Hospital Accounting System.