This retrospective study evaluated the effect of surgical computer-assisted navigation in temporomandibular joint (TMJ) ankylosis gap arthroplasty. Eighteen patients (25 sides) with bony ankylosis who underwent surgical treatment under computer-assisted navigation (navigation group) from May 2011 to April 2013 were assessed, along with 19 such patients (25 sides) treated without computer-assisted navigation (non-navigation group) from March 2009 to April 2011. The navigation group patients underwent surgery with the preservation of ≥3mm bone thickness in the skull base and anterior wall of the external auditory canal. Postoperatively, computed tomography (CT) was used to measure the residual bone thickness in the skull base and anterior wall of the external auditory canal. Maximum mouth opening (MMO) changes were evaluated at >1 year of follow-up. Postoperative CT measurements showed that the lowest skull base thickness in the navigation group was significantly lower than that in the non-navigation group (3.86±1.95mm vs. 6.01±3.07mm, P=0.009). The lowest thicknesses of the anterior wall of the external auditory canal were similar in the two groups. Postoperative follow-up showed similar average MMO in the two groups. Therefore, with the navigation system, TMJ ankylosis gap arthroplasty can achieve more extensive removal of the ankylosed bone, at least towards the skull base, under the premise of ensuring a safety distance of 3mm.