Performance evaluation of complex manufacturing systems is challenging due to many factors such as system complexity, parameter uncertainties, problem size, just to name a few. In many cases when a system is too complex to model using mathematical formulas, simulation is used as an effective alternative to conduct system analysis. A manufacturing system is a good example of such cases where both system performance and system complexity are greatly impacted by material handling (MH) strategy, management, and operational control. In this paper, we study vehicle general assembly (GA) system with MH, and focus on developing an efficient simulation method for modeling and analysis where traditional simulation methods may suffer from computation intensity. Making use of the partial system decomposability, we introduce an aggregated event-scheduling simulation method with two-level framework. A dividing mechanism with boundary conditions is employed in top-level simulation to divide the global event list into small sizes. A timing-focuses strategy based on max-plus algebra is applied in bottom-level local simulation to further reduce local event lists. With this new method it is possible to mimic real production systems fast and accurately within a reasonable computational time frame. The effectiveness and efficiency of the new simulation method are validated through experimental results.