The midpalatal suture acts as the growth centre of the maxilla. Colony-stimulating factor 1 receptor (CSF1R) is essential for osteoclastogenesis. Deletion of CSF1R, and its ligand, results in significant craniofacial phenotypes but has not been studied in detail in the midpalatal suture. Pregnant ICR mice were treated with the CSF1R inhibitor PLX5622 at embryo Day 14.5 (E14.5) to E17.5. Pups at E18.5, postnatal Day 3 (P3) and P7 were collected for skeletal and histological staining. Osteoclasts were labelled using TRAP staining. PHH3 and TUNEL were employed to detect cell proliferation and apoptosis. Sox9, Ihh, and Col10a1 and Runx2, Col1a1, and DMP1 were used to detect chondrogenic differentiation and osteogenic differentiation, respectively. CD31, MMP9 and CTSK were utilized to assess vascular invasion and osteoclast secretion enzymes, respectively. Embryonic inhibition of CSF1R resulted in a depletion of TRAP-positive cells and an enlarged cartilage zone of the midpalatal suture of postnatal mice. Compared to those in the control group, Sox9, Ihh, Col10a1, Runx2 and Col1a1 were upregulated, whereas TUNEL and DMP1 were decreased in this zone. In the trabecular region, Col10a1 was upregulated, while TUNEL, Col1a1 and DMP1 were downregulated. Moreover, the expression of MMP9, CTSK and CD31 was decreased, and invasion into the cartilage zone was delayed. Embryonic inhibition of CSF1R led to an abnormally enlarged cartilaginous zone in the midpalatal suture, potentially due to delayed endochondral ossification caused by the depletion of osteoclasts. Additionally, we established a novel model of midpalatal suture dysplasia, offering prospects for future research.