Abstract In order to address the problems of high empty rate and long waiting time of cross-level four-way shuttle during its operations, it is necessary to fully optimize the level of cooperation between shuttles and hoisters. Considering the variable speed of the four-way shuttle and the hoister in the movement process, with the objective of minimizing the total operation time of the inbound and outbound order tasks, a mixed integer planning model for the joint scheduling of the four-way shuttle and the hoister is established. An improved whale optimization algorithm is proposed in combination with the actual constraints of the four-way shuttle and hoister in the warehouse order picking process, and compared with simulated annealing, genetic algorithm, and an improved chimpanzee optimization algorithm. The results show that the designed algorithm has much better solution quality and effectively reduces the time in completing given order picking task.