Background: The human head is an integrated biological structure composed of the brain, cranial bones, facial structures, neuromuscular systems, and sensory organs, all interconnected through coordinated signaling. The relationship between brain development, function, and craniofacial growth is most evident after birth, during which the head increases approximately fourfold in size before adulthood. Brain morphology and volume are associated not only with neurological disorders but also with cognitive and behavioral characteristics. For example, children with holoprosencephaly often present with varying degrees of facial anomalies, while studies have shown that adolescents with malocclusion exhibit higher levels of anxiety, depression, and psychological stress. With the increasing availability of magnetic resonance imaging (MRI), it has become an essential diagnostic tool in clinical practice. MRI is particularly advantageous in pediatric populations due to the absence of ionizing radiation and its superior soft tissue contrast. Recent advances in image processing techniques have enabled comprehensive analysis of both brain structures and craniofacial morphology from a single MRI dataset, forming the basis of this study. Aim: To investigate the relationship between brain tissue volumes and maxillary hypoplasia using MRI-based voxelbased morphometry in children with neurological conditions. Materials and Methods: This study was conducted at the School of Biomedicine, Mongolian National University of Medical Sciences, in collaboration with Chifeng University, as part of the project titled “Investigation of the relationship between craniofacial anomalies and brain disorders using MRI”, funded by the Ministry of Education and Science. Voxel-based morphometry (VBM) analysis was performed on brain MRI scans of children aged 9–11 years. Results: Among the 25 children included in the study, 17 (68%) were male. The youngest average age was observed in the maxillary hypoplasia group (8.4±0.95 years). The signal-to-noise ratio (SNR) of MRI was lowest in the non-temporal epilepsy group (41.1±1.35) and higher in the maxillary hypoplasia group (49.6±8.22). Both epilepsy and maxillary hypoplasia groups demonstrated physiological asymmetry of the cerebral hemispheres, with left parietal lobe dominance (−0.1% and −0.3 cm, respectively). Right frontal lobe dominance (+1.1%) was observed only in the epilepsy group. Conclusion Children aged 9–11 years with maxillary hypoplasia showed a reduction in both gray and white matter volumes of the brain. These findings highlight the importance of early diagnosis of neurodevelopmental disorders affecting odontogenesis and emphasize the need for a multidisciplinary team-based management approach.