Due to the ability to differentiate into numerous cell types, multipotent mesenchymal stem cells (MSCs) are currently researched widely including in the field of craniofacial tissues engineering where always requires a wide variety of cell types and tissues while complete surgical reconstruction of craniofacial tissues is always difficult to achieve based on conventional therapies due to such high complexity. Nowadays, numerous animal model studies have been reported on the effect of MSCs in craniofacial tissue engineering including bone, tendon, cartilage, cutaneous wound and vascularization repair etc. Several clinical trials also have been reported with inspiring results. In this review, we will summarize the recent progress of MSCs in craniofacial tissue engineering and the potential clinical application in future.