In continuous evolution, sub networks (cliques) will be gradually formed in the alliance network. Taking cliques as a carrier, companies will learn from each other, and knowledge flow occurs. This paper combined cliques and knowledge flowto explore the impact of coupling between cliques and knowledge flow in the alliance network on innovation capability by using the alliance data of semiconductor industry in China and negative binomial regression. This paper found that the firm innovation capability will be stronger when the number of internal links in cliques is more without considering the characteristic of the alliance network; The cited and cite numbers will promote the firm innovation capability; As a adjustment variable, cliques have a negative regulation function between knowledge flow and firm innovation capability.This paper contributed to having a better understanding of the alliance network structure, and provided suggestions for the high-tech industry to improve enterprise innovative capability.