This paper studies the scheduling problem about the Automatic Vehicle Storage and Retrieval System controlling of the shuttle combined vehicles and the elevator to complete the storing and picking-up operations on the order in automatic three-dimensional warehouse. For the order with the pure storing operations or pure picking-up operations, it directly solve them similar to Traveling Salesman Problem(TSP), and for storing and picking-up compound operations,it will respectively cooperate and schedule the elevator with one or two sets of shuttle combined vehicles to complete the task in the shortest time. Pertinent mathematical models has been established, and have been simulated and optimized with MATLAB. Compared with the conventional random access strategy, the current method can greatly save the travel time of the elevator and shuttle bus. The lower time consumption and higher efficiency indicates that the method presented is of significant value in both theory and practical usage.