A model of scenario-based line capacity expansion problem for PWB (Printed Wiring Board) assembly systems at the aggregate level is developed. The model synthesizes BOM (Bill Of Material) of product families and machine operation flexibility, thus it is an attempt of integrating strategic capacity planning, aggregate production planning and MPS (Master Production Scheduling), which is an important research topic of production management. Since the resulting model is a large-scale two-stage stochastic mixed integer programming problem, it can not be solved with standard code. An approximate solution procedure is developed, which first reduces the searching space of capacity expansion decision variables to rough addition sets by heuristics, then the rough addition sets are searched through adaptive genetic algorithms. Numerical experiments are presented to show the financial benefit of the model and the feasibility of our approach.