Fractures within granite may become channels for fluid flow and have a significant impact on the safety of waste storage. However, internal aperture variation under coupled conditions are usually difficult to grasp, and the inevitable differences between the measured data and the real fracture structure will lead to erroneous permeability predictions. In this study, two different CT (Computed Tomography) image processing methods are adopted to grasp internal fractures. Several CT images are extracted from different positions of a rock sample under different confining stresses. Two critical factors, i.e., aperture and the contact area ratio value within a single granite fracture sample, are investigated. Results show that aperture difference occurs under these two image processing methods. The contact area ratio value under two image processing methods has less than 1% difference without confining stress. However, there is larger than ten times difference when the confining stress increases to 3.0 MPa. Moreover, the edge detection method has the capability to obtain a relatively accurate internal fracture structure when confining pressure is applied to the rock sample. The analysis results provide a better approach to understanding practical rock fracture variations under various conditions.