With the functional hazard analysis (FHA) approach applied to hazard identification of turbo-fan engine full authority digital electronic control (FADEC) system, the key problems of the system hazard identification and the multiple failure analysis efficiency are focused in this paper. A system function definition and accordingly a multi-layer failure analysis are proposed to remove the failure condition and effect analysis difficulties in FHA of FADEC system, due to the structural and functional complexity. A worse-combination filtering analysis skill is proposed to handle the quantity explosion problem in the multiple failure condition identification. Based on the basic principles of the Society of Automotive Engineers (SAE) ARP-4761 and all the above skills, a practicable hazard identification procedure is developed for the FHA implementation of FADEC systems and put into use in an industrial case. The results show that the proposed FHA procedure can help clearly identify the hazardous failure conditions of the FADEC system and effectively lower the task load in the multiple failure identification.