The safety analysis of the fly-by-wire control system with control allocation has been performed on the basis of system theory process analysis (STPA) method in this paper. Considering its complexity, conventional safety analysis techniques focus only on failures and redundant backups of critical components. STPA can consider software and human factors in the analysis process, and the output of this methodology includes unsafe scenarios to be considered in the early design. In this paper, control laws and control allocation are designed based on B747 aerodynamic data and identify the Unsafe Control Actions (UCA). Hazard causation scenarios from analysing UCAs demonstrate that the methodology can comprehensively and completely identify the potential hazards of the system, and provide effective suggestions and references for the safety design of civil aircraft with control allocation.