In order to improve the delivery rate of automated pharmacies and realize the shortest delivery time of drugs with multiple delivery documents. Based on the structure of a hospital automated pharmacy delivery system, a time scheduling model of multiple delivery task documents is established. An improved hybrid whale optimization algorithm (H-WOA) is designed for this model. Firstly, multiple drug delivery documents are integrated and grouped, and the crossover and mutation of genetic algorithm are integrated to improve the diversity of population exploration. Secondly, the affinity determination principle of antibody and antibody of immune cloning algorithm is introduced to help construct the best execution sequence. Finally, the encirclement contraction and spiral update mechanism of the whale algorithm are combined to ensure that the population finally converges to the best whale position. The implementation results show that the efficiency of H-WOA optimization algorithm is improved by 6.11% and 18.11% respectively compared with the original algorithm and the algorithm without optimization. It has the same optimization effect on the scheduling optimization of 4 or 5 delivery documents. It is proved that the improved algorithm has good optimization ability.