Under the new pattern of international and domestic double circulation, the scale of China's port logistics enterprise cluster is expanding, but the innovation difficulty of cluster enterprises is increasing sharply, the innovation power of core technology is insufficient, there are some problems, such as focusing on agglomeration rather than cooperation, the integration of industrial chain and innovation chain is not close, and the choice of innovation path is improper. The method and purpose of this paper are based on the theory of collaborative innovation, establish a structural equation model, empirically test the logistics clusters with ports above designated size in China, and put forward the key path for the collaborative innovation of port logistics enterprise clusters, and improve the collaboration degree and innovation performance of cluster enterprises. The empirical results show that the external environment of collaborative innovation (EECCI), the innovation learning ability of cluster enterprises (ILACE) and the cluster enterprises cooperation (CEC) can directly or indirectly affect the cluster collaborative innovation performance (CCIP), and the innovation learning ability of cluster enterprises (ILACE) plays a mediating role between the external environment of collaborative innovation (EECCI) and the cluster collaborative innovation performance (CCIP). Port logistics enterprise clusters need to develop environmental governance, knowledge governance, information governance and other mechanisms to promote collaborative innovation in the industrial chain, technology chain and value chain.