O-GlcNAcylation is a post-translational modification involved in various cellular processes, including cell cycle progression, signaling, transcription, and stress response. Mouse salivary gland morphogenesis shows specific localization patterns of O-GlcNAc transferase (OGT) and O-GlcNAc in developing acinar cells, suggesting a potential involvement of O-GlcNAcylation in acinar cell differentiation-related signaling molecules. To define its underlying mechanisms, this study used an OGT inhibitor, OSMI-1, and small interfering RNA (siRNA) targeting OGT, during in vitro cultivation of submandibular glands and assessed morphological and molecular alterations using histology, immunohistochemistry, Western blot, and RT-qPCR. As expected, OGT inhibition impaired terminal bud morphogenesis and altered cellular physiology. OSMI-1 treatment disrupted acinar cell differentiation, reflected by changes in expression patterns of signaling molecules crucial to acinar cell differentiation, including Sox9, Sox10, E-cadherin, and Mist1. Altered expression patterns of cytokeratins, including CK14 and CK18, confirmed altered ductal morphology. Therefore, our findings highlight the essential role of OGT-mediated O-GlcNAcylation in salivary gland morphogenesis with post-translational regulation of key signaling molecules governing functional differentiation of acinar cells.