The analysis of occlusal relationship is important for the success of dental treatment. Three-dimensional (3D) computer models of upper and lower dental casts can play a significant role. In this study, we proposed and applied a new method in actual clinical assessment to measure dental casts with occlusal relationship by using a micro-focus X-ray CT system. We examined the modelling accuracy by comparing multiple 3D images taken by shifting the dental cast position. Modelling accuracy was confirmed as 0.03 mm. One occlusal treatment in clinical practice was selected as a case example. The dental casts and bite impression, taken before treatment, were scanned and the occlusal contacts and distance distribution between the upper and lower casts were visualized by a coloured map and overlaid on the computer models. Distances between the upper and lower casts of selected points were compared before and after the treatment. Initially, the subject had early contact on the anterior teeth, where distance was measured as 0.04 mm, and only one area measured less than 0.15 mm. After treatment, five areas measured less than 0.15 mm. Also, by comparing the dental cast models taken before and after occlusal adjustment of the tooth, the position and amount of adjustment were visualized. We successfully demonstrated the quantitative clinical assessment of occlusal treatment.