To an aircraft, the accuracy of aerodynamic configuration has a direct influence on flight performance. To improve the assembly accuracy of aircraft wing components, two kinds of positioning method and the corresponding assembly precision are studied, and a low-cost flexible assembly tooling system for different wing components is proposed. First, the article analyzes the technological characteristics of airplane wing skin and determines the assembly requirement. Second, positioning method based on contour boards and coordination holes and their assembly precision are researched. Third, to verify the positioning method and the algorithm of assembly precision calculation based on coordination holes, a locating unit with three motion axes is designed and manufactured. Fourth, experimental verification is done and the corresponding results are analyzed. Experiment results showed the assembly precision based on coordination holes has an improvement of 24% contrasting with the precision based on contour boards, and the assembly productivity is increased by 60%. The flexible assembly tooling system also has a demonstration effect for other flexible assembly tooling within the aerospace industry.