Inventory management in cluster supply chains is a new organization mode. A hybrid control method is applied to solve the complex multi-modes issues. The different control strategies on variable stock condition in supply chains are discussed in details. By simulation cases, the paper presents the procedure of directing the optimal decision variables. The results proves the bullwhip effect in cluster supply chains can be weaken and the order fluctuation tends to be easily stable by exerting hybrid control and across-chain inventory cooperation.