Modern hospital pharmacies are undergoing broad-scale shifts toward informatization and automation. With the widespread use of automated medicine dispensing systems in major Chinese hospitals, their application value has been increasingly confirmed. However, relative to other countries, automation of China’s pharmacies was relatively delayed, and the use of imported automated equipment in domestic hospital pharmacies dealing with an enormous prescription burden poses substantial challenges in maintaining high automation efficiency when the hospital patient flow is at its peak. Objective to optimize the medicine storage system of automatic medicine dispensers and to improve the automation efficiency of pharmacies using the entry-item-quantity (EIQ)-ABC analysis method and a track utilization rate algorithm. Methods A total of 76,069 prescriptions from the CONSIS automated medicine dispensing system of medicine dispensing system of our hospital’s outpatient pharmacy were selected in June 2020, and the EIQ-ABC analysis method was used to perform associative classification of the dispensing volume and frequency of each medicine. The varieties of medicines in the automatic dispenser were adjusted according to the classification results, and then, the storage space of medicines was optimized using a track utilization rate algorithm. The performance of this method was evaluated by comparing the automatic rate of the dispensing volume, and the real-time window dispensing rate and prescription ratio before and after optimization. Results After the implementation of the EIQ-ABC analysis method and track utilization rate algorithm, the average automation rate of dispensing volume, real-time window average dispensing rate, and real-time window average prescription ratio increased by 2.46%, 4.4%, and 4.87%, respectively, which were significantly higher than those before implementation (P < 0.05). Conclusion Using the EIQ-ABC analysis method and the track utilization algorithm to optimize the varieties and storage space of medicines in an automatic medicine dispenser can fully utilize storage space, reduce instances of lack of medicine in the dispenser, and improve the fully automatic dispensing rate.