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The fast growing computer technology had been successfully applied to the industry and medical applications. The operation efficiency, system accuracy, and quality consistency can be significantly improved by introducing the computer techniques. In recent years, several works combine the techniques of the computer software, machine vision and image processing to assist the surgeons to improve the surgical quality. Especially, the surgery navigation system is more emphasized than ever. In this paper, we propose a computer aided retained auricular prosthesis surgery system. In this work, a 3D digitizer is used to measure the coordinate and posture of the patient. The patient's coordinate is further transformed to the coordinate of the computer model. In addition, a sound-based navigation system is developed to guide the surgeon to reach the registration position that was identified at the pre-surgery stage. Finally, a clinical case of the retained auricular prosthesis surgery of the microtia children was proposed and successfully validated.