During the last decade, the remotely-controlled ships had developed rapidly because of the potential advantages of improving safety, reducing emissions, and reducing manning. Due to the safety of remotely-controlled system is the important foundation in the research for remotely-controlled ships, this paper proposed a remotely-controlled system for different levels of autonomy and with or without crew on board. And the safety of the system is analyzed by using the system-theoretic process analysis (STPA) approach. The analysis results indicate that: (1) Among the 13 types of system-level hazards, virtual captain failure, remotely-controlled station failure and communication error have the largest number of unsafe control actions, and the number of corresponding safety strategies is also the largest, which accounts for more than 10%; (2) The potential risk failures of the remotely-controlled system of inland ships mainly include five categories: hardware equipment failure, system software failure, communication factor, human error and environmental factor; (3) When the level of autonomy is improved, the risk of collision and wave damage caused by communication error will be reduced or eliminated. And the number of effective safety strategies will also increase, while the number of safety strategies will decrease; (4) When there are crews on board, the number of most effective safety strategies will increase by 10, and the total number of safety strategies will increase by 20. The results are helpful to improve the safety of the remotely-controlled system of inland ships in the preliminary design stage, by designing the safety strategies for different autonomy levels and with or without crew on board.