In this paper, the performance of a typical composite work cell structure that includes multiple machines and a material handling gantry is studied. A mathematic model is established to analyze the performance of such gantry systems. Due to the unique features of the gantry system, cycle time and waiting time of the gantry and machines are discussed and formulated based on two basic scenarios. To measure the impact of disruption events, permanent production loss is evaluated by using the sensor data collected from plant floors. Data-driven diagnostic methods are developed to identify the bottleneck machine and to evaluate permanent production loss attribution of each machine. The results provide a solid base to efficiently and effectively improve the performance of a composite work system. Performance diagnostics of gantry systems provides a theoretical and practical basis for production improvement. A gantry system for composite lay-up processes is used for numerical simulation case studies, by which the performance diagnostic methodologies and improvements are demonstrated.