Background: A thorough understanding of the root canal morphology of primary molars is highly important for pulp treatment of primary teeth. The purpose of this study was to elucidate age-related changes in the root canal morphology of primary molars and determine new indices to determine the root canal anatomy via cone-beam computed tomography (CBCT). Methods: CBCT data of primary molars from 58 children aged 3–8 years without systemic diseases that affect tooth development were collected. The following indices were defined and calculated using Mimics 17.0, 3-Matic 9.0, and ImageJ software: (i) the cross-sectional area of the root canal; (ii) R.15: the proportion of the lateral canal wall with an inner diameter less than 0.15 mm; (iii) LC /LR: the ratio between the canal length and root length; and (iv) Ndis: the discontinuous canal count. Correlation analysis and binary logistic regression were performed to assess the variants and age-related changes in canal morphology. Results: On CBCT analysis, the cross-sectional areas of the mesiobuccal (MB) root, palatal (P) root and distobuccal (DB) root canals were negatively correlated with age (p < 0.05), with correlation coefficients of −0.41, −0.42 and −0.26, respectively. The R.15 of MB roots was positively correlated with age (p < 0.05, rs = 0.39). The LC /LR values for the MB, DB and P roots decreased with age, with correlation coefficients of −0.39, −0.42 and −0.29, respectively (p < 0.05). The risk of discontinuous canals for MB, DB and P roots increased with age (p < 0.05), with odds ratios of 1.61, 1.48 and 1.60, respectively. Conclusions: The new indices developed in the present study based on CBCT successfully demonstrated age-related changes in the root canals of primary molars.