The aim of this study was to investigate the anatomical features of the maxillae and vomer in patients with bilateral cleft lip and palate (BCLP). Craniofacial measurements of 24 adult BCLP patients (GB) and 32 normal adult controls (GN) were carried out. We measured the width and length of the maxillae, their relative positions with respect to the coronal plane passing through the basion, and the volume, length, cross-sectional area, and mean width of the vomer. Between-group differences were assessed using independent-sample t tests. Finite element models (FEMs) were used to explore the bite forces acting on the bone by evaluating the distribution of stress and bone displacement. The mean vomer volume and width were significantly larger in the GB group than in the GN group (P = 0.000), whereas the length was significantly shorter (P = 0.000). The anterior maxillary length (A1-P3M⊥CP) was significantly larger in the GB group (P = 0.013), whereas the posterior maxillary length (P3M-P6M⊥CP) and overall maxillary length (A1-P6M⊥CP) at the dental level were significantly reduced (P < 0.01). In the BCLP FEM analysis, the maximum displacement was on the left premaxillary edge (0.2 mm), and high Mises stresses were found in the superior region of the vomer (22.4 Mpa), high tensile stresses in the inferior region (14.3 Mpa), and significant compressive stresses in the superior region (−24.7 Mpa). In summary, for BCLP patients, forward growth of the maxillae and vomer was inhibited during maxillary development, and the vomer was thicker and its volume was increased compared with the vomer in normal subjects.