The invention discloses a goods location allocating method applied to an automatic warehousing system of a multi-layer shuttle vehicle. The method comprises the following steps: firstly, according to the quantities of goods shelves and tunnels, generating plane layout structure data of the system; then analyzing the waiting time of the shuttle vehicle executing an outbound task as well as the idle time of a hoister; establishing an open queuing network model for describing the system; analyzing the relationship among the waiting time of the shuttle vehicle, the idle time of the hoister and the time of inbound and outbound works by a decomposition process; determining that the higher the reaching rate of a task serviced by the shuttle vehicle is, the lower the goods location of the task is, and the goods with highest correlation are allocated at different layers, so that multiple shuttle vehicles can provide service simultaneously; finally putting forward a principle of dividing storage zones in light of item correlation, establishing a correlation matrix of outbound items, clustering the items by an ant colony algorithm, and combining and arranging the storage zones in a two-dimensional plane according to the analysis result of the queuing network model, thereby realizing the allocation of goods location. By the method, the waiting time of the shuttle vehicle and the idle time of the hoister can be effectively shortened, so that the rate of equipment utilization and the throughput capacity of a distribution center are increased.