Composite patch repair of aircraft structural panels has recently received wide attention. When this repair technique is applied to the aircraft structural panels, it is imperative to design composite patches which are reliable enough to operate in severe environmental conditions. In designing composite patches, the accurate stress fields in the repaired structural panels and the bonded composite patches should be analyzed since highly complicated three-dimensional stress fields are developed. To obtain the accurate stress fields in repaired structural panels and bonded composite patches, usually the conventional three-dimensional finite element method is used. However, the conventional three-dimensional finite element method involves with a long computational time for iterative stress analysis. In this paper, we develop an effective three-dimensional finite element method based on the concept of domain decomposition with independent interfaces. Using this method, we carry out several parametric studies to examine the effect of patch shape and size on the stress fields in a repaired structural panel and bonded composite patches. The method is also used to determine the optimum patch shape and size so as to endure maximum tensile applied stress by a mathematical programming.