When conducting batch inbound and outbound operations in a planar mobile three-dimensional garage, the different order of system commands and the detention position of Rail guided vehicles (RGVs) can change the interaction time between the elevator and RGVs, as well as the utilization rate of RGVs, which will affect the overall inbound and outbound operation time of the system. To reduce the operation time of the three-dimensional garage, a real-time warehouse location information model was established for the operation process of the planar mobile three-dimensional garage. A collaborative operation model between the car elevator and the RGV was established, and the warehouse location coordinates in the RGV outbound command were adjusted under dynamic time thresholds. Then, taking the homework time as the objective function, an improved Grey Wolf algorithm is proposed for solving. The simulation results show that compared with the original grey wolf algorithm and genetic algorithm, the improved grey wolf algorithm has better performance in optimization and robustness, and can effectively shorten the operation time of the planar mobile three-dimensional garage, improving the efficiency of inbound and outbound operations.