The design technology for civil aircraft has already become more and more important. Because of the need for aircraft’s structure and function, the aircraft structure engineers can design many smallsize cutout structures on the skin panel of aircraft’s fuselage. The quality of such smallsize cutout structures can directly affect physical mechanical performance and weight for the airplane, etc. The design of smallsize cutout structure is an important part of the aircraft’s design process, and a successful aircraft must have an excellent design of the smallsize cutout structure. Based on a certain type of aircraft, the design procedure of the fuselage smallsize cutout structure has been analyzed and discussed detailedly in this article. Load analysis, design of relevant components, seals and surface protection, etc are also studied concretely in this paper.