Reducing logistics costs in the supply chain has been a key concern of major enterprises. Meanwhile, reducing the delivery cost of the supply chain is a key component of supply chain cost management. Therefore, this article mainly focuses on the cost management of agricultural enterprise supply chain delivery and achieves the goal of reducing logistics costs by optimizing the specific process of supply chain delivery. Firstly, a multi-objective mathematical model was established by comprehensively considering multiple objectives such as delivery cost targets and carbon emission targets in the delivery process of agricultural products. Furthermore, the delivery quality of agricultural products during the delivery process was ensured through time window constraints, and corresponding constraint conditions were established based on the actual scenarios during the agricultural product delivery process. On this basis, an Improved Artificial Bee Colony algorithm (IABC), a heuristic algorithm, was designed. And simulation experiments were conducted. The simulation results showed that the algorithm designed in the article can be effectively applied to the cost management problem of agricultural enterprises.