The terminal area is a region in civil aviation transportation where unsafe incidents are highly prone to occur. The terminal area control system, as a crucial part of the air traffic control system, is essential for conducting safety risk research on its operational processes. A risk analysis method combining system theoretical process analysis (STPA) with cross impact analysis and interpretive structure model (CIA-ISM) was proposed to address the strong coupling of security risks in terminal area control systems and the difficulty of quantifying the interaction effects between risks using traditional analysis methods. Firstly, STPA was used to identify 20 safety risk factors within the system. Secondly, the Pearson correlation coefficient method was employed instead of the traditional Delphi method to eliminate subjective biases, and the impact intensity between risk factors was quantified using 200 historical accident data to construct a cross-impact matrix. Finally, through the ISM model, risk levels were divided and the influence of unsafe states during the operation of the terminal area control system on the probability of accidents was deduced, thereby analyzing the key risk factors of the terminal area control system. Taking a specific terminal area control system as an example, scenario deduction reveals the dynamic mechanism by which the probability of accidents approaches 1 under multi-factor coupling, verifying the effectiveness of the model. The results show that improper coordination among control teams and other direct causes account for 84% of the accident probability, with improper coordination among control teams, coordination issues with adjacent control rooms, handover problems, and errors in intelligence data published by controllers being the three most significant direct risk causes affecting the safe operation of the terminal area control system.