The anatomical variability of primary molars promotes research to improve clinical restorative activity, forensic identification, and industrial development. The objective was to study the morphology of the pulp chamber and its three-dimensional relationship with the external morphology of the tooth. A total of 151 deciduous molars were collected and subjected to three-dimensional imaging analysis in order to determine dental crown (CV) and pulp chamber (PV) volumes, their ratio (VR), pulp chamber roof (PCR) and pulp chamber floor (PCF) area, the furcation length (FD), and morphological peculiarities. The data were compared using the Kruskal–Wallis test in SPSS 26 software. The statistical analysis determined statistically significant differences between the four groups of molars for all variables. Great anatomical variability was observed, especially in the maxillary first molar, the volumes were higher in the maxillary second molar and the highest risk of furcal perforation was seen in the mandibular first molar. Additionally, mandibular second molars with six pulp horns, and some different density images compatible with accessory canals and pulp stones were found. Based on the findings of this investigation, we confirm the great anatomical variability that exists between the maxillary and mandibular molars.