Lithium-ion battery energy storage system (BESS) has rapidly developed and widely applied due to its high energy density and high flexibility. However, the frequent occurrence of fire and explosion accidents has raised significant concerns about the safety of these systems. To evaluate the safety of such systems scientifically and comprehensively, this work focuses on a MW-level containerized lithium-ion BESS with the system-theoretic process analysis (STPA) method. The work identified 53 unsafe control actions and corresponding loss scenarios. By combining loss scenarios and expert evaluation opinions, the key risk factors for system operation are obtained. Finally, this work proposed corresponding countermeasures and suggestions to address the key risk factors and improve the safety and reliability of the entire system operation. This work discusses the operational risks of MW-class containerized lithium-ion BESS and provides technical guidance for engineers in system designs, safe operations, and engineering applications.