Taking a three-level, multi product, and dual channel supply chain as an example, the inventory control problem in the supply chain under stochastic demand was explored. A dual channel supply chain simulation model was established based on the independent control, information sharing, and pre warehouse replenishment model of “single manufacturer-dual distributor-dual retailer-dual customer”. In node enterprises, the Pull/Push strategy was adopted for ordering decisions, and information entropy was used to measure the uncertainty of nodes. Finally, the whale optimization algorithm was used to adjust the inventory control parameters in the simulation model. The results show that in the case of interruption, the pre warehouse replenishment mode can increase customer satisfaction in the interrupted channel by 80%. The whale optimization algorithm can ensure customer satisfaction while controlling total costs and reducing uncertainty in the supply chain system.