A new automatic warehouse sorting system, the crane & shuttle based storage and retrieval system (C&SBS/RS), is proposed in this paper. In C&SBS/RS, the crane-based storage and retrieval system (CBS/RS) in the pallet storage area provides the pallets picking, the shuttle-based storage and retrieval system (SBS/RS) in the tote storage area handles the cases and items picking. When the inventory in SBS/RS is lower than safety stock, SBS/RS initiates replenishment transaction. Besides, the order matrix is proposed to study order structure parameters, such as the order density, the order strength, the wave size and so on. Moreover, this paper analyzes the influence of order structure on the replenishment with four evaluation parameters, e.g., the workload of CBS/RS and SBS/RS, the number of used storage position in SBS/RS, the replenishment time. Numerical experiments are carried out to analysis the impact of the wave size and the proportion of high turnover SKU on those four evaluation parameters under multiple order structure, which is to help warehouse operation manager decide replenishment strategy parameters.