This study is to investigate the anatomical features of maxillae in unilateral cleft lip and palate (UCLP) patients with maxillary retrusion. Additionally, the dissimilarities of retruded maxillae between the UCLP patients and the skeletal class III patients were compared. Craniofacial measurements were carried out among 32 UCLP adult patients with maxillary retrusion (GC), 24 adult patients in class III (SNA < 80°, ANB < 0°) patients (GIII), and 32 normal controls (GN). The authors measured the width and length of the maxillae, as well as their relative positions to the coronal plane passing through basion. The independent sample group t test was performed, and P < 0.05 was regarded as statistically significant. In the GC group, the anterior and posterior maxillary length (A1-P3M⊥CP and P3M-P6M⊥CP) and overall maxillary length (A1-P6M⊥CP) at the dental level, the interdental widths of the maxillae, the maxillary volume (GM), and the volume consisting of maxilla and maxillary sinus (GT) significantly reduced compared with the GN group (P < 0.05). The distances from the points on the maxillae to the coronal plane (A1⊥CP, P3M⊥CP, and P6M⊥CP) in the GC and GIII groups were smaller than those in the GN group (P < 0.05). In summary, for the UCLP patients, the decreased prominence of maxillary complex could be mainly caused by the shortened maxillary length; meanwhile, posterior position of the maxillary body may have some influence on the maxillary protrusion. While for the class III patients, maxillary retrusion was resulted from malposition and malmorphology on an equal basis.