Focusing on a hydropower-seawater desalination symbiosis system implemented in a coastal steel enterprise, this study addresses the challenges of using exhaust steam from a steam turbine as the heat source for low-temperature multi-effect desalination. In this highly coupled configuration between the steam turbine generator set and the desalination unit, coordinated safety control remains difficult and lacks mature technical solutions. To ensure equipment safety, this paper proposes a set of safety control strategies tailored to the symbiosis process, including start-up logic, equipment safety interlock protection under failure conditions, and mode-switching protection for the desalination unit under low steam turbine load. These strategies establish bidirectional interlock protection between the steam turbine generator set and the desalination unit. Application of the proposed control scheme in an actual coastal steel plant verifies its effectiveness. The strategy enables safe and orderly start-up and achieves bidirectional emergency shutdown when either subsystem fails, allowing desalination shutdown induced by turbine failure and vice versa. Concurrently, it accommodates large-scale load fluctuations in the plant’s gas supply, significantly enhancing operational safety.