Background: Craniofacial abnormalities, such as cleft lip and palate (CL/P), pose functional and aesthetic challenges that require multidisciplinary care, including orthodontic treatment. This study investigates the impact of orthodontic interventions on tooth morphology, alignment, arch symmetry, and occlusal relationships in patients with craniofacial abnormalities over a six month period at Azra Naheed Dental College. Methodology: A total of 73 patients were selected using purposive sampling. Data were collected through clinical examinations, patient records, and radiographic analyses. Measurements of tooth alignment, arch form, and occlusal relationships were taken pre- and post-treatment. Statistical analyses, including descriptive statistics, paired t-tests, chi-square tests, Pearson’s correlation, and multiple regression, were applied to evaluate treatment outcomes. Results: Orthodontic treatment significantly improved tooth alignment, arch symmetry, and occlusal relationships (p < 0.05). A mean reduction in tooth misalignment by 2.5 mm was noted in 80% of patients. Cleft lip and palate patients showed more complex orthodontic challenges, resulting in lower success rates compared to other groups. Pre-treatment alignment and craniofacial severity were significant predictors of treatment outcomes. Conclusion: The study highlights the effectiveness of orthodontic treatment in improving dental parameters in craniofacial abnormalities, though limitations such as a small sample size and observational design underscore the need for further research.