Although the thymus and parathyroid glands originate from the third pharyngeal pouch, their postnatal relationship has been predominantly interpreted in embryological terms, with limited structural evidence supporting a functional interaction. The aim of this study was to explore whether multimodal observations support a previously underrecognized structural relationship between the thymus and parathyroid glands. For this purpose, microCT-based three-dimensional reconstruction was used to assess their spatial and branching high-attenuation structures, and the findings were correlated with histomorphometric analysis, immunohistochemical evaluation of vascular and extracellular matrix markers, scanning electron microscopy (SEM), and available clinical data. MicroCT analysis revealed distinct three-dimensional architectural patterns in thymic and parathyroid tissues. Histomorphometric and immunohistochemical findings revealed stromal organization and molecular expression patterns compatible with tissue remodeling. SEM provided additional microarchitectural detail, supporting the presence of structural continuity. Notably, the integration of three-dimensional imaging with histological and ultrastructural data revealed a previously underrecognized level of organization at the parathyroid–thymus interface. The overall findings indicate a more complex organized anatomical and microvascular relationship rather than a simple juxtaposition of two distinct structures. Taken together, these multimodal findings support the hypothesis of a previously underexplored structural relationship between the thymus and parathyroid glands. However, the proposed microarchitectural framework should be considered exploratory and requires validation using dedicated vascular imaging and morphometric techniques. The observed micro-tissue-specific architecture suggests that an organized structure may facilitate inter-structural communication, potentially resembling a port system-like arrangement. Further studies are required to clarify its physiological relevance.