This paper introduces a comprehensive methodology for the assessment, safe operation, and supervision of mechatronic systems. The objective is to systematically analyse mechatronic systems and establish effective supervisory frameworks. To achieve this, we leverage the Safe-Structured Analysis Design Technique (Safe-SADT) formalism to evaluate overall system reliability and the Grafcet modeling approach to capture control-command aspects in mechatronic systems. We also outline the practical steps involved in implementing WinCC for mechatronic system supervision. This methodology empowers in-depth exploration of mechatronic systems during the design phase.