A breakthrough innovation has become a powerful weapon to win the competition, and breakthrough innovation has the characteristics of high investment, high risk, so that enterprises tend to reduce the investment and risk for innovation alone through knowledge sharing and innovation alliance. This paper uses evolutionary game method to analyze the knowledge sharing among organizations in a breakthrough innovation alliance. Conclusion: reducing the cost of inputs, enhancing punishment coefficient, expanding knowledge input, and improving the knowledge absorptive capacity can effectively promote the innovation alliance's knowledge sharing to enhance the level of enterprise breakthrough innovation.