Aside from the human and managerial skills necessary to propel any business, the right Lean deployment can play a big role in reducing waste and maximizing efficiency. Capturing these benefits is highly dependent on adequate Lean techniques integration. Companies shifting towards Lean conversion have tried one of many Lean Manufacturing optimization tools at their disposal today (JIT, Pull System, U cells, CrossTraining, Visual Management, SMED, Poka Yoke, etc.) hoping to capture the benefits of such conversion. One of the major hurdles these companies face is the difficulty to choose the Lean tools that best fit their economic contexts and that are best tailored towards reaching their productivity or quality milestones. The Discrete Event Simulation becomes an interesting approach, to imitate the evolution of a manufacturing system and to represent the transformation induced by the Lean tools integration in the manufacturing line. The system developed in this paper is a Co-Simulation system. It is built based on a two-level structure. The first level is a basic framework for modeling the manufacturing assembly line with its various components (using JaamSim), while the second is a hierarchical framework for executing parallel Lean Tools simulations (using MECSYCO). To demonstrate the usefulness of this Co-Simulation system, an example of an Aeronautic Assembly Line is used. Three Lean Configuration Scenarios are investigated under market fluctuation context (Batch Policy, Setup times reduction with SMED, Pull System), compared with an Actual model simulated as a Lean Free scenario.