Currently, R&D investment of government is increased dramatically. However, the budget of the government is different depend- ing on the size of ministry and priorities, and then it is difficult to obtain consensus on the budget. They did not establish decision support systems to evaluate and execute R&D budget. In this paper, we analyze factors affecting research funds by linear regression and decision tree analysis in order to increase investment efficiency in national research project. Moreover, we suggested strategies that budget is estimated reasonably.