Based on the analysis of the operational character of supply chain resource integration under 4PL, and the dominant factors and the relations among them, the analysis on integration risk which makes great effect on supply chain resource integration decision process is given in this paper. The resource integration decision mode which has been introduced into the integration risk of supply chain system is put forward. Then, the extended integration decision optimization model of supply chain resource integration under 4PL and the improved optimization ant algorithm are put forward to solve this decision process. At last, the reasonability and feasibility of the method is discussed via the case simulation. The optimization model and algorithm of this paper exhibits the operational advantage of 4PL, emphasizes the risk equilibrium of supply chain resource integration from strategic and systemic perspective and facilitates the balance of multiobject in integration optimization at the same time.