The performance of a green supply chain shows particularity and complexity due to its multiple network features. This study aiming at digging out the logical relationship between network embedding and green supply chain performance in the context of agglomeration scenarios. In this study, taking Chinese eco-industrial park as the sample, the logic and mechanism of multiple network embedding on the performance of the green supply chain under the agglomeration scenario are empirically investigated by mediation and moderation as well as simulation method. As a result, the three dimensions of network embedding: relationship embedding, structure embedding and knowledge embedding, all significantly promote the integration of green knowledge, and green knowledge integration plays a mediating effect between multiple network embedding and green supply chain performance. As a whole, the agglomeration scenario plays a positive moderation role in logic chain of "multiple network embedding—knowledge integration—green performance" in green supply chain; to be specific, the economic performance of the green supply chain shows a trend of first improving and then stabilizing, while the environmental performance shows a "U" pattern. In conclusion, it is crucial to embed platform for knowledge integration and interaction into the industrial agglomeration and explore cooperation network of the green supply chain. By integrating the internal and external knowledge resources of the agglomeration through multiple network embedding, we can effectively and efficiently realize sustainable development and cleaner production in a green supply chain.