With the rapid development of the aviation manufacturing industry, automatic drilling and riveting technology has been widely applied in aircraft assembly. Facing the demand for automated and flexible assembly technology, higher standards have been set for tooling design. This paper focuses on an in-depth exploration of the flexible tooling design technology for automatic drilling and riveting equipment. Firstly, the pre-assembly requirements of aircraft panel/half-lober components and the technological requirements of automatic drilling and riveting are clarified, and the functional requirements of the flexible tooling in the technological process are sorted out. Secondly, the design theory of flexible assembly tooling is discussed. Combining with the system architecture diagram of the flexible tooling, the composition of the software and hardware modules of the flexible tooling is introduced. Finally, combined with the design cases of flexible tooling for 20 configuration components in a certain project, the transmission structure design, modular structure design, and quick-change structure design of the flexible tooling are elaborated in detail. The research results provide theoretical support and practical reference for the flexible tooling design of automatic drilling and riveting equipment, and help to promote aviation assembly technology to a new level.