At present, as result of development concepts and old management mode of industrial economy do not conform to research law in the knowledge economy times, and contradiction between market-oriented research project and research personnel of government staff status is hard to coordinate, so outstanding problem in the current research funds management is that regulation on personnel funds management is incompatible with production law of knowledge product and incentive mechanism for human capital, it is reflected in the following three aspects: a) Intellectual input is not linked to research project funds and research project funds fail to provide enough positive incentive effects; b) Regulation on personnel costs which does not conform to reality needs is difficult to implement; c) The lack of intellectual input compensation mechanism results in unspoken rules rife in use of research funds. For this purpose, we should strengthen design of Incentive Mechanism for scientific research personnel in research projects.