Abstract:After the analysis of the relevant literature,the paper selects financial support efficiency evaluation as a break-through to strengthen the path of China＇s megaproject of science research management．After the study on the current sit-uation of fiscal investment,it finds that the fund is in good condition,the expenditure structure is basically reasonable,thediversified investment mechanism is basically established,and the basic establishment of the financial fund managementsystem is established．At the same time,through DEA and Malmquist model,it evaluates the comprehensive efficiency ofthe decision-making unit value and efficiency value．The results of empirical studies show that,fiscal in support of majorprojects in the process of the development of resource allocation efficiency isn＇t optimal．There is optimization space．In re-cent years,through technical innovation,resource allocation,scale efficiency and other ways to optimize management,theeffect is obvious．In fact,quality factors mainly include that powers lack of a clear definition,and powers and expenditureresponsibilities do not match,organization management system needs to be improved,and implementation of the modellacks a clear judgment．Recommend continuous improvement major special financial investment and management,it sug-gest that we should match megaproject of science research powers and expenditure responsibilities,sound mechanisms forimplementation and optimize the management structure．