The model-based safety analysis (MBSA) has become increasingly mature since its inception and is more suitable for complex civil aircraft systems. On the basis of current research and ARP4761A draft, the MBSA method is used to study the failure assessment method of civil aircraft during the operation phase. Compared to traditional methods, integrating operational data, functional failures, and equipment failures into the same model is more convenient for conducting operational failure assessment. Firstly, this paper defines the basic elements of the operational failure assessment model and sorts out the model construction process, and establishes equipment level, system level, and aircraft level models containing failure modules based on Simulink. The external lighting sub-system of a certain aircraft model was taken as an example to build the model, and a numerical analysis was conducted on the operational data of a certain fleet. The results show that the the error between MBSA and FTA results is within an acceptable range. At the same time, the FMEA analysis was performed, and the probability of loss of landing lighting function hazard was calculated and simulated using operational data. 30 simulation results indicate that the probability of occurrence based on operational data fluctuates around the design value, slightly exceeding the overall design value, but still meeting the safety requirements.