Cleft palate is one of the most common birth defects. Previous studies revealed that multiple factors, including impaired intracellular or intercellular signals, and incoordination of oral organs led to cleft palate, but were little concerned about the contribution of the extracellular matrix (ECM) during palatogenesis. Proteoglycans (PGs) are one of the important macromolecules in the ECM. They exert biological functions through one or more glycosaminoglycan (GAG) chains attached to core proteins. The family with sequence similarity 20 member b (Fam20b) are newly identified kinase-phosphorylating xylose residues that promote the correct assembly of the tetrasaccharide linkage region by creating a premise for GAG chain elongation. In this study, we explored the function of GAG chains in palate development throughWnt1-Cre; Fam20bf/fmice, which exhibited complete cleft palate, malformed tongue, and micrognathia. In contrast,Osr2-Cre; Fam20bf/fmice, in whichFam20bwas deleted only in palatal mesenchyme, showed no abnormality, suggesting that failed palatal elevation inWnt1-Cre; Fam20bf/fmice was secondary to micrognathia. In addition, the reduced GAG chains promoted the apoptosis of palatal cells, primarily resulting in reduced cell density and decreased palatal volume. The suppressed BMP signaling and reduced mineralization indicated an impaired osteogenesis of palatine, which could be rescued partially by constitutively activeBmpr1a. Together, our study highlighted the key role of GAG chains in palate morphogenesis.