Heterogeneous systems consist of a multitude of system components, which are derived from different physical and technical domains. The complexity of this components constantly increases thereby. For the functionality of the heterogeneous overall system the faultless interaction of these system components and frequently also the interaction with the physical influences of the environment are of crucial importance. In this thesis computer-aided design methods are examined, which support the validation of the system functionality, the verification of the separate design steps and the optimization of the heterogeneous system during a model-based top-down design. In particular for the range of microsystems and the range of mechatronic systems with hardware/software coupling simulation-based methods are presented, which facilitate a continuous model-based design of such systems.