The aim of this study was to investigate the prevalence of tooth agenesis, tooth malformation, and eruption patterns of upper canines/first premolars in Taiwanese children. A total of 132 cleft lip and cleft palate (CLCP) patients (82 boys and 50 girls) underwent alveolar bone grafting (ABG) between 2012 and 2022. The patients' dental records and X-ray images were inspected. We examined dental anomalies, including congenital missing teeth, microdontia, and transposition from the upper canines to the upper first premolars in these CLCP patients. Additionally, we investigated the mean ABG operation age (9.27 ± 0.76 years) of our patient; 40.9% of them received pre-ABG orthodontic treatment at 8.72 ± 0.70 years. Among the 132 cleft subjects, the prevalence of tooth agenesis is 73.5% (97/132). The most frequently missing teeth are the maxillary lateral incisors (right side: 46.2%; left side: 47.0%). In this study, microdontia are found in all the upper incisors, of which the highest percentage (18.9%) is observed in the upper left lateral incisors. The prevalence of upper canine and first premolar transposition is 10.6%. The pattern of tooth agenesis and microdontia of the upper lateral incisors shows a strong correlation with the cleft sites of these CLCP patients in our study. These results may support the idea that the patterns of dental anomalies in CLCP patients are region-specific.