A mechatronic system is an assembly of technological components, such as a mechanism, sensors, actuators, and a control unit. Recently, a number of researchers and industrial manufacturers have highlighted the potential advantages of lightweight parallel mechanisms with respect to the accuracy, dynamic performances, construction cost, and transportability issues. The design of a mechatronic system with such a mechanism requires a multidisciplinary approach, where the mechanical deformations have to be considered. This thesis proposes two original contributions in this framework. (i) First, a modular and systematic method is developed for the integrated simulation of mechatronic systems, which accounts for the strongly coupled dynamics of the mechanical and non-mechanical components. The equations of motion are formulated using the nonlinear Finite Element approach for the mechanism, and the block diagram language for the control system. The time integration algorithm relies on the generalized-alpha method, known in structural dynamics. Hence, well-defined concepts from mechanics and from system dynamics are combined in a unified formulation, with guaranteed convergence and stability properties. Several applications are treated in the fields of robotics and vehicle dynamics. (ii) Usual methods in flexible multibody dynamics lead to complex nonlinear models, not really suitable for control design. Therefore, a systematic nonlinear model reduction technique is presented, which transforms an initial high-order Finite Element model into a low-order and explicit model. The order reduction is obtained using the original concept of Global Modal Parameterization: the motion of the assembled mechanism is described in terms of rigid and flexible modes, which have a global physical interpretation in the configuration space. The reduction procedure involves the component-mode technique and an approximation strategy in the configuration space. Two examples are presented: a four-bar mechanism, and a parallel kinematic machine-tool. Finally, both simulation and modeling tools are exploited for the dynamic analysis and the control design of an experimental lightweight manipulator with hydraulic actuators. A Finite Element model is first constructed and validated with experimental data. A reduced model is derived, and an active vibration controller is designed on this basis. The simulation of the closed-loop mechatronic system predicts remarkable performances. The model-based controller is also implemented on the test-bed, and the experimental results agree with the simulation results. The performances and the other advantages of the control strategy demonstrate the relevance of our developments in mechatronics.