A good cyber-physical-systems (CPS) design methodology must conduct trade-off analysis of both the physical characteristics of the CPS as well as its cyber sub-system in a holistic manner. This paper presents a design space exploration (DSE) approach for CPSs that emphasizes the variabilities of the physical subsystem and control aspects of the system. We propose the application of parameterizable physical models and automatic recalculation of control algorithm parameters for the explored systems. The resulting parameterizable models can be applied in a systematic simulation-based DSE framework that facilitates the identification of superior system configurations. We applied the proposed design flow to a real non-linear inverted pendulum system with a range of physical and cyber settings. The results show the feasibility and effectiveness of our approach in the design of physical and control parts of CPSs. Our work supplements existing work on cyber system modeling and plays an integral part in the design automation of such systems.