The work aims to design the system dimensions to maximize the storage space, when the input/output ports of the system are at the midpoint of the bottom of the rack. The mathematical model of the dual-command cycle travel time of the 3D compact system was established. It was assumed that the input/output ports of the system were at the bottom of the rack, and the discussion was carried out in six situations to study the design problem of the input/output ports of the automatic storage system. Based on the solution optimized by the model, type 5 was selected (a*=1.1, b*=0.63). When the ratio of length to width to height of the system was 1.1∶0.71∶1.2, the running efficiency of the stacker was the best. From the simulation, when the rack dimensions of the 3D compact system (length:width:height ratio) is 1.1∶0.71∶1.2, the expected travel time of the system under the dual-command cycle is the least, namely the 3D compact system performs the dual-command cycles operation at this ratio for the shortest time.