The embedding behavior of supply chain enterprises in cooperation is crucial to efficiently integrate on-chain resources to improve collaborative innovation performance, however, the relationship between the two has not yet reached a consistent research conclusion. In this paper, 60 related literatures, 118 effect sizes and 17911 independent samples were used as research objects to explore the overall effect of network embedding (including relational embedding and structural embedding) and collaborative innovation performance, and subgroup analysis was used to clarify the moderating effect of moderating variables in the relationship between the two. The results show that network embedding and its sub-dimensions have a significant positive correlation with collaborative innovation performance. In addition, differences in industry type, location factors, performance type, and empirical research methods all lead to inconsistent research results. To a certain extent, this study provides a theoretical basis for the research on the relationship between network embedding and collaborative innovation performance, and also provides reference ideas for supply chain enterprises to improve their innovation ability through network embedding.