In rock engineering projects, professionals assess the overall rock mass qualities using a sole value. However, the true qualities of partial rock masses are incompatible with such a value. To address this problem, the idea of regionally classifying rock mass qualities is proposed and the associated procedure presented. To achieve this goal, the probabilistic and deterministic joints within the study area were determined, and a three-dimensional joint network model was created. Then, the three-dimensional joint network model was discretised into interlocking subdomains, and the modified blockiness index (MBi) was used to finely identify the homogeneous structural regions, together with the k-means algorithm and the sum of squared errors (SSE). A synthetic model comprising homogeneous structural regions was developed and validated with respect to the extracted cross-sections. Next, an improved Rock Mass Rating system (RMRmbi) was introduced, and the viability of RMRmbi was supported through a significant amount of theoretical cases and several real cases. Finally, visualisation of regional RMRmbi classification results was performed. Results show that: (i) the homogeneous structural regions are finely demarcated in three dimensions; and (ii) the proposed idea can overcome the problem of rock mass quality classification using the conventional approach often leading to ‘overgeneralisation’.