The hydro-mechanical behavior of rock mass in natural barriers is a critical factor of interest, and it is mainly determined by the characteristics of the fractures distributed in the rock mass. In particular, the aperture and contact area of the fractures are important parameters directly related to the fluid flow and significantly influence the hydro-mechanical behavior of natural barriers. Therefore, it is necessary to analyze the aperture and contact area of fractures distributed in potential disposal sites to examine the long-term evolution of the natural barriers. This study aims to propose a new technique for analyzing the aperture and contact area using the natural fractures in KURT (KAERI Underground Research Tunnel), an underground research facility for the deep geological disposal of high-level radioactive waste. The proposed technique consists of a matching algorithm for the three-dimensional point cloud of the upper and lower fracture surfaces and a normal deformation algorithm that considers the fracture normal stiffness. In the matching process of upper and lower fracture surfaces, digital images obtained from compression tests with pressure films are used as input data. First, for the primary matching of the upper and lower fracture surfaces, an iterative closest point (ICP) algorithm is applied in which rotation and translation are performed to minimize the distance error. Second, an algorithm for rotation about the x, y, and z axes and translation in the normal direction is applied so that the contact area of the point cloud is as consistent as possible with the pressure film image. Finally, by applying the normal deformation algorithm considering the fracture normal stiffness, the aperture and contact area of the fracture according to the applied normal stress are derived. The applicability of the proposed technique was validated using 12 natural fractures sampled from KURT, and it was confirmed that the initial apertures were derived similarly to the empirical equation proposed in the previous study. Therefore, it was judged that the distribution of apertures and contact areas according to applied normal stress for laboratory-scale fractures could be derived through the technique proposed in this study.