Innovation failure knowledge sharing plays an important role in reducing the probability of repeated failure of subsequent innovation and improving innovation ability of virtual research organization. However, it is very difficult for members to actively share the innovation failure knowledge without incentives. To promote the sharing behavior of innovation failure knowledge in virtual research organization, by using game theory, considering the risk aversion degree of members and the negative effect of fault-tolerance environment, the incentive model of innovation failure knowledge sharing of virtual research organization was constructed, the incentive relationship of innovation failure knowledge sharing between organization and its members under the influence of different states was analyzed, and the theoretical model was simulated and verified through a case study from China. Results show that: (1) without considering the negative effect of fault-tolerant environment, the optimal incentive coefficient of innovation failure knowledge sharing is positively related to the shareable rate and the transformation ability of innovation failure knowledge of members, and negatively related to the sharing cost and risk aversion degree of members; (2) considering the negative effect of fault-tolerant environment, virtual research organization should make a corresponding modification of sharing incentive intensity according to the estimation of tolerance degree to fault-tolerant environment by itself and its members, so as to reduce the knowledge input of organization. The findings obtained from this study provide a novel idea and method for the design of incentive mechanism of innovation failure knowledge sharing of virtual research organization.