Aim: To investigate the root canal morphology of hypomineralised second primary molars(HSPM) using micro-CT(μCT) compared with non-hypomineralised second primary molars (non-HSPM). Methodology: Ten HSPM and 10 non-HSPM were divided into Group 1(maxillary HSPM), Group 2 (mandibular HSPM), Group 3(maxillary non-HSPM), and Group 4 (mandibular non-HSPM). All teeth were scanned using μCT to assess the following parameters: (i) root canal configuration, (ii) pulp volumes, and (iii) the influence of the root canal system landmarks on access cavity outline forms and canal curvature. Two-way ANOVA was employed for descriptive analysis (P < 0.05). Results: At the furcation level, there was minimal variation in the number of canals. In the mesiobuccal root, Group 1 showed higher frequency of multiple canals in the middle (85.7%) and apical (85.7%) thirds compared with Group 3. In the mesial root, Group 4 demonstrated multiple canals at the furcation (60%) compared with Group 2(33.3%). In the distal root, Group 2 demonstrated a higher percentage of multiple canals at the apical level (100%) compared with Group 4. The mean pulp volumes of Group 2 and Group 4 were 54.1 mm3(16.7) and 30 mm3(5.12), respectively, which was statistically significant (P < 0.05). The canal curvature values did not differ significantly between HSPM and non-HSPM groups. Conclusions: HSPM exhibited greater variations in their root canal configuration when compared to non-HSPM.