Based on the social network analysis by using the survey data, we analyze the relationship between innovation network structure of Shouguang vegetable and Yanling flowers and trees cluster, so as to understand the role of agricultural cluster innovation network mechanism. The analysis shows that：l）Each cluster innovation network of network structures has different characteristics. The enterprises of Shouguang cluster are more closely related, while Yanling cluster has more core nodes within the agglomeration network; 2）The Government-Industry-University-Research cooperation innovation networks have similar characteristics. The performance of the whole network connection is weak, the network structure hole＇ s characters are not significant, and the limit of node structure hole is more balanced; 3）The regional innovation network has similar characteristics, network structure hole features are prominent, and the limit of node structure hole is large; 4）In international cooperation and innovation, the motivation that Shouguang enterprises communicate with international counterparts is more significantly; Yanling cluster＇ s network structure hole features are more prominent, and the control on external resource is stronger. The further analysis shows that, cooperation network of cluster enterprises is the basis of other innovation networks. The agricultural industry cluster innovation mainly comes from the heterogeneous resources bringing by the weak ties of the cluster and then absorps and diffuses in the cluster through the strong correlation.