In the digital era, logistics supply chain scheduling has become the key to enhancing the competitiveness of e-commerce, and the fine management and scheduling optimization of the e-commerce logistics supply chain is particularly important. Based on the three-layer supply chain scheduling model, the study combines the production cost, transportation cost, and transportation time of each member of the supply chain with other influencing indexes. It establishes a multi-stage supply chain scheduling model (SCISM) with dual-objective. The rotational algorithm in linear programming is used to solve the model after it has been constructed. The effectiveness of the SCISM model for intelligent e-commerce logistics supply chains is explored through algorithmic and arithmetic validation of the SCISM model. The results show that the SCISM model algorithm determines the optimal solution