The stacking fault in crystals of GaN was studied by high-resolution electron microscope images in combination with image deconvolution. The principle of deconvolution for high-resolution electron microscope images is briefly introduced. It is demonstrated that an image originally does not intuitively reflect the examined crystal structure can be transformed into the structure image. The stacking faults in crystals of GaN were observed with the high-resolution microscope. The image deconvolution was performed for the image, and the atomic configuration in the defect core is seen clearly in the deconvoluted image. Based on this, the type of stacking fault has been determined. Besides, the effectiveness of image deconvolution in studying crystal defects is discussed.