The aim of the article is to propose a complex methodology for implementing a safety analysis of dynamical systems. The safety analysis is performed in the process of control system development, especially aiming at safety-critical processes of system operation. The methodology was divided into seven basic steps. The individual steps of the methodology are carried out in a hierarchical sequence. The step “Preliminary Hazard Analysis” consists of the PHI and PHA methods. Further, roles of individual methodology steps are detailed. In the second part of the article, the principle of safety-critical process monitoring based on models is.