Recently, along with the increasing of the government investment for hi-tech plan projects, the moral hazard originated from these science research institutes becomes more and more severe. Designing a set of appropriate mechanisms for the incentive and restraint to improve the research efficiency of these institutes is desiderated. Based on the principle-agent theory, an incentive contract model for staged investment in hi-tech plan projects is established, and the staged strive levels of these science institutes are analyzed. Then, the role of staged investment and incentive contract for mitigating moral hazard of the sciense research institutes is reseached. Finally, some suggestions for the investment management of hi-tech plan projects are put forward.