Improving enterprise innovation performance is key for enterprises to obtain sustainable competitiveness. With the increasingly fierce market competition of technological and product innovation, acquiring external heterogeneous knowledge of alliance enterprises becomes core to improving innovation performance. In this paper, we constructed a theoretical model to present the effect of inter-enterprise knowledge heterogeneity and alliance network governance mechanisms on enterprise innovation performance. We selected high-tech enterprises as the research object for empirical research and reached the following conclusions: (1) Inter-enterprise knowledge heterogeneity has a positive effect on exploratory and exploitative innovation performance, and (2) trust and contract have a moderating effect on the relationship between inter-enterprise knowledge heterogeneity and enterprise innovation performance.