Initiating event identification is the primary task in safety analysis based on accident mechanism. The comprehensiveness and the completion of identification have a direct effect on final results. Due to the width of related facets and multitude of impact factors, an operable systematic method is required to guide the identification process. Aiming at the properties of missile weapon, the MLD (master logic diagram) was proposed to provide a systematic hierarchical description of missiles. It was also utilized to collect and classify identified initiating events. For the first time, the HAZOP (hazard and operability analysis) was introduced in missile system safety analysis to identify the initiating events. Combined with FMEA (failure modes and effects analysis), this framework provided support for the identification of initiating events which were caused by single failure or parameter abnormity. Results show that the proposed framework provides a practical way to ensure the comprehensiveness of initiating event identification for system safety analysis of missile weapon.