Four-way Shuttle Automated Storage and Retrieval System (FWS-AS/RS) is a storage form widely used in industries such as e-commerce, pharmaceuticals, and food in recent years. It has the characteristics of flexible system configuration, high storage density, high efficiency, and high automation. To efficiently design the shelves layout and equipment configuration of FWS-AS/RS, this paper firstly considered the possibility of arranging shelf rows, columns, and layers under different storage scales and discussed the impact of changes in horizontal aisle layout position and quantity as well as different shelf depths on operational efficiency. Then, taking the different configurations of shuttle cars and lifts as well as the different placement positions of lifts and input/output (I/O) ports as variables, it established the motion models of shuttle cars and lifts considering acceleration, deceleration, no-load, load energy consumption, and energy recovery during braking; it used the total cost, transport distance, energy consumption, and space utilization rate as evaluation indicators. Through simulation experiments, regular design strategies were obtained for constructing four-way shuttle style stereoscopic warehouse shelves, including row, column, layer, depth, tunnel position, number and position of I/O ports, the ratio of four-way shuttle cars (FWS) to lifts, and the relationship between lifts and longitudinal tunnels. Finally, taking a storage capacity of 5 000 as an example, the study applied these strategies to design simulation. The simulation results show that the three optimization schemes reduced the transport distance, energy consumption, total cost, and floor area by an average of 43.30%, 57.69%, 11.17%, and 8.60%, while increasing the space utilization rate by an average of 5.66%, thus verifying the correctness of the design strategy. The design strategy can provide reference for the construction and operation of such stereoscopic warehouses.