Due to the importance of the commercial aviation system and, also, the existence of countless accidents and unfortunate occurrences in this industry, there has been a need for a structured approach to deal with them in recent years. Therefore, this study presents a comprehensive and sequential model for analyzing commercial aviation accidents based on historical data and reports. The model first uses the failure mode and effects analysis (FMEA) technique to determine and score existing risks; then, the risks are prioritized using two multi-attribute decision making (MADM) methods and two novel and innovative techniques, including ranking based on intuitionistic fuzzy risk priority number and ranking based on the vague sets. These techniques are based in an intuitionistic fuzzy environment to handle uncertainties and the FMEA features. A fuzzy cognitive map is utilized to evaluate existing interactions among the risk factors, and additionally, various scenarios are implemented to analyze the role of each risk, group of risks, and behavior of the system in different conditions. Finally, the model is performed for a real case study to clarify its applicability and the two novel risk prioritization techniques. Although this model can be used for other similar complex transportation systems with adequate data, it is mainly employed to illustrate the most critical risks and for analyzing existing relationships among the concepts of the system.