The present research envisages a novel group decision making model to evaluate the operational risk of airports from four aspects of human, equipment, management and environment factors. The proposed model featured an integration of intuitionistic fuzzy set and set pair analysis. Due to the lack of the systematic data and quantitative analysis concerning the uncertainty of these indicators, an intuitionistic fuzzy set was used to characterize them, which converted them into the ternary connection numbers based on set pair analysis. A new distance based on the intuitionistic fuzzy set and set pair analysis was proposed to analyze the consistency degree of any two experts on the same airport operation risk, wherein the degree of contact determined both the uncertainty and certainty of each indicator, so as to obtain the ranking degree of the expert group on the operation risk of all airports. Moreover, the relationship between the value of these indicators and the threshold changes of the airport operation risk ranking was evaluated. This study could be used as an effective tool for transit authorities to rank the operational risk of different airports, by comprehensively considering the viewpoint deviation of different decision makers on the same scheme, and its uncertainty factors. The analysis of the case study comprising four airports in China showed that with an increase in the degree of contact, the operation risk value of the airport in Beijing remained the same that of Tianjin and Qinhuangdao decreased, and for Shijiazhuang gradually increased.