This study aimed to assess the prevalence and distribution pattern of dental anomalies in the permanent teeth of patients with non-syndromic cleft lip with or without cleft palate. Additionally, it aimed to compare differences in dental anomalies between cleft and non-cleft areas, considering gender and cleft phenotype. Panoramic radiographs of 164 patients diagnosed with non-syndromic orofacial clefts were retrospectively analyzed by a single examiner to confirm dental anomalies. The dental anomalies investigated included tooth agenesis, supernumerary teeth, microdontia, rotation, ectopic eruption, and enamel hypoplasia. Cleft phenotypes were categorized into 7 types based on medical and dental records. A significantly higher prevalence of supernumerary teeth was observed in males than females within non-cleft areas (p = 0.017), with no significant differences in other dental anomalies. In non-cleft area, patients with cleft palate exhibited a high prevalence of tooth agenesis (p < 0.0001) and microdontia (p = 0.012) compared to other cleft phenotypes. Maxillary incisor rotation was closely associated with adjacent tooth agenesis in unilateral cleft lip and palate cases (p = 0.034). This study suggests that the additional subphenotype based on dental anomalies in patients with orofacial cleft may serve as applicable clinical markers.