In this thesis, the COMAC ARJ21 fuselage’s final assembly process is used as a case study. High production rate (i.e. number of aircraft assembled per year) with reasonable cost is the overall aim in this example. The output of final assembly will essentially affect the prior and subsequent processes of the overall ARJ21 production. From the collected field data, it was identified that a number of disruptions (or bottlenecks) in the assembly sequence were caused by breakdowns and maintenance of the (semi-)automatic assembly machines like portable computer numerical control (CNC) drilling machine, rivet gun and overhead crane. The focus of this thesis is therefore on the maintenance strategies (i.e. Condition-Based Maintenance (CBM)) for these equipment and how they impact the throughput of the fuselage assembly process. The fuselage assembly process is modelled and analysed by using agent-based simulation in this thesis. The agent approach allows complex process interactions of assembly, equipment and maintenance to be captured and empirically studied. In this thesis, the built network is modelled as the sequence of activities in each stage. Each stage is broken down into critical activities which are parameterized by activity lead-time and equipment used. CBM based models of uncertain degradation and imperfect maintenance are used in the simulation study. A scatter search is used to find multi-objective optimal solutions for the CBM regime, where the maintenance-related cost and production rate are the optimization objectives. In this thesis, in order to ease computation intensity caused by running multiple simulations during the optimization and to simplify a multi-objective formulation, multiple Min-Max weightings are applied to trace Pareto front. The empirical analysis reviews the trade-offs between the production rate and maintenance cost and how these objectives are influenced by the design parameters.