The aim of the present study was to clarify the shape of the pulp chamber and the three-dimensional positional relationship between the contour of the crown and pulp chamber using a micro-computed tomography system (micro-CT) for restorations of mandibular second deciduous molars without pulp exposure, and to evaluate quantitatively the thickness of the hard tissue surrounding each pulp chamber. Samples were caries-free mandibular second deciduous molars of the deciduous and mixed dentition periods (10 each) extracted from the dry skulls of Indian children. Micro-CT images of the crowns were taken. Horizontal two-dimensional slice data were then stacked to construct three-dimensional images, and the shape of the pulp chamber and positional relationship between the contour of the crown and pulp chamber were observed from various directions. Then, the volume ratio of the pulp chamber relative to the crown contour and the distance from the crown surface of each pulp horn (hard tissue thickness) were investigated to evaluate the characteristics of the deciduous and mixed dentition periods objectively. The results showed that the mesiobuccal and mesiolingual pulp horns of deciduous dentition were most pointed, and approximately the same height. The pulp horn was lower and rounder in the mixed dentition period than in the deciduous dentition period. The pulp chamber shifted to the mesial side of the crown contour in both the deciduous and mixed dentition periods. These findings suggest that care should be exercised to avoid exposure of the mesial pulp horn during cavity preparation for deciduous mandibular second molars, especially during the deciduous dentition period.