The cooperation between enterprises is actually at a certain risk of interruption, which has a significant impact on the robustness of manufacturing service system (MSS). Evaluating MSS' robustness is integral to production and service provisioning, and thus the influence mechanism should be clearly revealed for assisting professionals in the company in improving the robust performance. In this paper, we present an effective methodology for explicating the impact of cooperation uncertainty on the robustness of MSS from a complex system standpoint. This methodology characterizes MSS as a topological network consisting of serval service subsystems, and constructs the measure metrics system of which the validity and applicability are proved theoretically from the dimension of structure and performance. Furthermore, it simulates the cooperation interruption from four different scenarios with algorithms, and finally takes an elevator manufacturing service network as the case to illustrate this novel methodology. The simulation findings suggest that identifying the critical paths in MSS and standardizing the cooperation mechanism within and among core manufacturing service principals outperform the other measures in improving the robustness of MSS.