The distributed material warehouse is the crucial link in the process of modern enterprise construction, and the goal of the enterprise is to save the cost of material distribution and reduce the time of distribution. In order to obtain the optimal ordering and allocation scheme, firstly, a distributed inventory system consisting of an ordering centre, a material coordination centre and n material warehouses are considered, and the cost model of ordering and allocation of the distributed material warehouse is established. Next, the safety stock and the ordering point of the distributed material warehouse are solved. Then the improved genetic algorithm-simulated annealing algorithm (IGA-SA) is used to solve the optimization of the distributed material warehouse. Finally, the application example is given. The results show that the IGA-SA algorithm can effectively reduce inventory cost and improve inventory utilization.