Time is the primary factor to the outcome of R&D project, so the client usually setup incentive mechanism to insure the project being completed on schedule, but there is no expert study on the optimization of incentive mechanism itself. In this paper, we define the conception of incentive mechanism, introduce incentive mechanism and flexible resource constraint to traditional resource constrained project scheduling problem to formulate incentive mechanism optimization model of R&D project from both sides of the contract. By solving the model we can obtain the optimal incentive intensity to given dead date. Both sides of the contract can attain maximal income under the schedule with the optimal incentive intensity. Ultimately, the outcomes of the paper are illustrated by an instance.