A supply chain inventory network system state transition model is presented, which includes the uncertainties of demand, production capacity, supply chain network structure and the lead time delays. To minimize the negative effect of bullwhip effect, a dynamic inventory control strategy and its economic performance indicators are proposed. Then a sufficient condition for the effective inventory control policy of the uncertain supply chain networks with lead time delays is given in terms of the linear matrix inequalities(LMIs). Simulation study shows the effectiveness and feasibility of the proposed inventory policy in reducing bullwhip effect.