Patients with unilateral cleft lip and palate (UCLP) could present with a notable nasal deformity with alar base retrusion, which should be considered when planning orthognathic surgery (OGS). This retrospective study included 84 patients with Class III malocclusion. Cone beam computed tomographic data were used for the investigation. 42 patients had complete UCLP, and the other 42 did not have a cleft. All the patients underwent preoperative virtual surgical planning. Preoperative and postoperative images were used to measure anteroposterior changes in the bone and soft tissue at the alar bases. In the UCLP group, varying degrees of alar base discrepancies were observed before surgery. In the piriform region of the cleft side, the bone was retruded in 32 cases, but the soft tissue was thicker in 38 cases, and the mean skin surface was anterior in 28 cases. After surgery, the bone discrepancy was not significantly changed (p = 0.288), however, the skin surface symmetry was improved (p = 0.013). Relating to the bone advancement, the ratio of soft tissue change was smaller on the cleft side than the noncleft side (0.56 ± 0.30 vs. 0.77 ± 0.33, p < 0.001). In the control group, a consistent ratio change was observed on both sides (0.76 ± 0.19 vs. 0.79 ± 0.27, p = 0.544). This study revealed improved alar base symmetry in patients with UCLP after OGS. The soft tissue change ratios were different across the cleft, which should be considered during treatment planning.