The presented dissertation deals with the modeling and implementation of distributed control systems in the context of cyber-physical systems. The dissertation is devoted to selected methods for modeling systems with discrete events, specifically to models of hybrid systems in the form of finite-state automata and Petri nets. The main goal of the dissertation is the proposal of a methodology for the modeling and analysis of distributed control systems in terms of throughput and response of communication interfaces and computing processes. The proposed methodology describes the procedure for performing an analysis of existing hardware and software resources within the framework of a distributed control system. Subsequently, it presents the procedure for creating a model of a distributed system composed of a combination of models of finite-state automata and Petri nets. In the last submodule, the methodology presents the possibility of using the created model to determine the throughput and response of the system, which can be used in the design and actual implementation of the distributed control system. The verification of the proposed methodology is demonstrated in three case studies that use the proposed methodology to create a complex subsystem model of the control system of the ALICE experiment at CERN and the application of mobile robotics within the distributed control system in CMCT&II at the DCAI FEEI TU workplace in Košice. Last but not least, the dissertation deals with the implementation of the software modules forming the software output of this dissertation, which are used within the detector control system of the ALICE experiment at CERN.