The invention relates to a model based on a cross-layer shuttle vehicle intensive automatic storage system and an optimization method of the model. Elevators and shuttle vehicles are respectively analyzed, and average service time models of the elevators or the shuttle vehicles at each stage in the stock output operation process of the cross-layer shuttle vehicle intensive automatic storage system are solved; according to the operation processes of the shuttle vehicles and the elevators, with a stock output task serving as a customer and the shuttle vehicles serving as service counters, and the shuttle vehicles serving as customers and the elevators serving as service counters, a multilevel semi-open-loop queueing network model is established for the stock output operation of the cross-layer shuttle vehicle intensive automatic storage system; an approximate average algorithm is used for solving the multilevel semi-open-loop queueing network model, and main performance parameters in evaluation indexes of the cross-layer shuttle vehicle intensive automatic storage system are obtained. By means of the model, the performance of the system under different goods shelf configurations can be accurately and effectively evaluated, the optimal shuttle vehicle and elevator configuration combinations can be obtained, and therefore the design of the system is guided, and the system running cost is saved.