This paper centers on the logistics and supply chain management of e-commerce enterprises, studies the development mode of e-commerce logistics as well as the logistics process, and constructs a collaborative innovation model of e-commerce logistics integration based on supply chain management. Through the synergistic composite system in the role of management activities, the harmonious coexistence between the various components of the subsystem order parameter in order to achieve the overall effect of the system. The dynamic evolution process of consumers, e-commerce platforms and logistics enterprises is simulated and analyzed, and the optimal decision-making under the integrated collaborative innovation mode is studied. The results show that under the platform warehousing + distribution integration synergy (SP) mode, the double marginal effect is 0.865, and both e-commerce platform and logistics enterprises reach a steady state at 0.723. The purpose of this paper is to propose innovative supply chain management and logistics warehousing solutions that can achieve cross-border e-commerce logistics integration based on supply chain management.