The success of craniomaxillofacial (CMF) surgery depends not only on the surgical techniques, but also upon an accurate surgical planning. However, surgical planning for CMF surgery is challenging due to the absence of a patient-specific reference model. In this paper, we present a method to automatically estimate an anatomically correct reference shape of jaws for the patient requiring orthognathic surgery, a common type of CMF surgery. We employ the sparse representation technique to represent the normal regions of the patient with respect to the normal subjects. The estimated representation is then used to reconstruct a patient-specific reference model with "restored" normal anatomy of the jaws. We validate our method on both synthetic subjects and patients. Experimental results show that our method can effectively reconstruct the normal shape of jaw for patients. Also, a new quantitative measurement is introduced to quantify the CMF deformity and validate the method in a quantitative approach, which is rarely used before.