The craniofacial region contains a variety of specified tissues, including bones, muscles, cartilages, teeth, blood vessels and nerves. Infections, traumas, genetic, anatomical, or congenital abnormalities could cause tissue defects in the region. Craniofacial tissue engineering and regeneration remain challenging problems for oral and maxillofacial surgeons and scientists. Stem cells isolated from the bone marrow, adipose tissue, dental pulp, the deciduous tooth, or the periodontium were proven to play an important role in tissue regeneration including craniofacial bone defect regeneration, facial nerve regeneration, TMJ (temporal-mandibular joint) condylar cartilage regeneration, TMJ disc regeneration and teeth regeneration in massive studies. In the review, the animal models for craniofacial engineering and regeneration are discussed. Specifically the modalities of establishing a defect model and treatment of the defect with various stem cells in combination with different cytokines and biomaterials are included. The review could be used to choose an appropriate experimental model for specific tissue defect, or to design innovative, reproducible, discriminative experimental models in the future.