The rapid expansion of maritime transport has led to the increased scale and complexity of vessels, making safety and environmental protection paramount for sustainable development. Electric propulsion systems offer notable advantages in terms of efficiency and emission reduction; however, they also present new safety challenges. Traditional reliability-based safety methods, which primarily address hardware failures, are inadequate for addressing risks associated with automation, control logic, and human–machine interaction. This study applies the System-Theoretic Process Analysis (STPA) methodology to identify hazards and analyze risks in the propulsion system of an electric vessel. By conceptualizing safety as a control problem, STPA facilitates the identification of hazards in complex socio-technical systems. The findings reveal that the safety of the propulsion system is mainly influenced by three factors: (1) the reliable functioning and communication between control subsystems; (2) crew decision-making during normal operations and emergency situations; and (3) the effectiveness of human–machine information exchange. Based on these insights, three areas for improvement are proposed: enhancing the automation and adaptability of control systems, strengthening crew training and emergency response capabilities, and optimizing human–machine interfaces and feedback mechanisms. The study demonstrates the applicability of STPA in guiding safety enhancements for electric vessel propulsion systems.