Cross-border passenger flow is the most important part of Zhuhai-Macao cross-border traffic, and it is the main reason that affects the analysis of Zhuhai-Macao cross-border traffic. From the perspective of passenger behavior selection, this paper uses the fuzzy set qualitative comparative analysis of multivariate interaction to explore the complex paths that affect the factors of the airport cooperation between Zhuhai and Macao. The study found that convenience is a necessary condition to promote the cooperation between Zhuhai and Macao airports; it has an integrated effect with the four factors: comfort, low cost, scientificity and additional functions. There are seven intermediates that promote the diversified cooperation between Zhuhai and Macao airports. Among all the combination paths, “convenience” enjoys greatest frequency, followed by “low cost”. Therefore, in order to make better use of the integrated effect of the conditional variables, the governments of Zhuhai and Macao should implement the positioning and division of labor requirements given by the Outline of the Development Plan for the Guangdong-Hong Kong-Macao Greater Bay Area, so as to achieve complementary advantages and win-win results. “Hard connectivity” of infrastructure and “soft connectivity” of customs clearance facilitation will improve the efficiency of factor circulation, promote the complementary advantages of tourism resources, build a tourism economic circle between Zhuhai and Macao, and provide driving force for the cooperation between the airports. The opportunity of constructing Guangdong-Macao in-depth cooperation zone in Hengqin should be seized in order to explore a new mechanism for deepening cooperation between Zhuhai airport and Macao airport.