Safety analysis is a significant step for safety-critical system development. Compared with traditional vehicles, the system interactions for autonomous vehicles are more abundant and complex. Traditional hazard analysis methods, such as failure mode and effects analysis (FMEA) and fault tree analysis (FTA) which are based on the component failure and reliability theory, cannot identify the system hazards related to system interactions. An emerging hazard analysis method based on systems theory, systems theory process analysis (STPA) mainly focuses on identifying the control system hazards caused by system interactions. In this study, STPA method is used to identify the potential hazards and casual factors for autonomous emergency braking systems by concentrating on system interactions. To improve the consistency between system design and safety analysis, the workflow combining model-based systems engineering (MBSE) and STPA is proposed. The systems modeling language (SysML) is used to describe control structure and system interaction relationships. According to the identified casual factors, certain constraints and requirements can be derived, which can provide the guidance for system development with respect to system design. Furthermore, the quantitative analysis of certain unsafe control action is conducted by simulation, which shows effectiveness and feasibility of the proposed method in safety analysis and system design.