We explored modularity and morphological integration of the ventral cranium during postnatal ontogeny in Martino’s vole (Dinaromys bogdanovi). Two closely related phylogenetic groups, originating from the Central and Southeastern part of the species range in the western Balkans, were considered. As expected, both phylogroups had similar patterns of ontogenetic changes in cranial size and shape variation, modularity and integration. At the level of within individual variation, the hypothesis that the viscerocranial and neurocranial regions are separate modules was rejected, indicating that the hypothesized modules are not developmental, but rather functional. At the level of among individual variation, the viscerocranium and the neurocranium could not be recognized as separate modules at the juvenile stage. The strength of association between the hypothesized modules becomes lower with age which finally results in a clear 2-module organization of the ventral cranium at the adult stage. On the other hand, patterns of morphological integration for the cranium as a whole, the viscerocranium and the neurocranium stay consistent across ontogenetic stages. The developmental mechanism producing integration of the cranium as a whole, as well as integration of the neurocranium, varies throughout postnatal ontogeny. In contrast, we detected the ontogenetic stability of the mechanism responsible for covariation of viscerocranial traits which could provide ongoing flexibility of the viscerocranial covariance structure for high functional demands during lifetime. Findings from our study most likely support the idea of the ‘palimpsest-like’ model of covariance structure. Moreover, similarity or dissimilarity in the patterns of within and among individual variation in different sets of analyzed traits and comparisons across ontogenetic stages demonstrate how studies on small mammals other than mice can give new insights into postnatal cranial development.