In this paper, knowledge sharing between enterprise and university in industry-university-research synergetic innovation is studied by constructing a stochastic differential game model involving stochastic disturbance. Dynamic programming method is employed to derive the equilibrium knowledge-sharing strategies and subsidy ratio both in Stackelberg game and cooperative game. By comparing the obtained results, we find that: (1) both in Stackelberg game and cooperative game, the more knowledge sharing cost and knowledge decay rate, the less knowledge is shared. The higher knowledge innovation ability and marginal profit, the more knowledge is shared; and (2) the optimal knowledge sharing, the total profit, the expected innovative knowledge and its variance of the cooperative game are higher than that of the Stackelberg game respectively.