Abstract Background This exploratory study aimed to evaluate the expansion effects of a customized elastodontic appliance (CEA) on maxillary and mandibular arches in mixed dentition children using cone-beam computed tomography (CBCT), and to clarify whether these effects are dental, dentoalveolar, or skeletal. Methods This retrospective study included 31 mixed dentition children (mean age 8.3 ± 1.2 years) who underwent CEA treatment for 8.2 ± 1.3 months. Pre- and post-treatment CBCT images were used to measure width changes at three levels: cusp, alveolar bone, and apical basal bone. Paired t-tests were used for comparisons. Results Significant increases were observed at cusp and alveolar levels. At the cusp level, maxillary inter-canine width increased by 2.97 mm ± 1.31 mm (95% CI: 2.49–3.45, P < 0.001), and mandibular inter-canine width by 2.39 mm ± 1.32 mm (95% CI: 1.91–2.87, P < 0.001). Maxillary second primary molar buccal cusp width increased by 1.67 mm ± 0.85 mm (95% CI: 1.36–1.98, P < 0.001), and mandibular counterpart by 1.26 mm ± 1.11 mm (95% CI: 0.85–1.67, P < 0.001). At the alveolar bone level, maxillary alveolar crest width increased by 1.39 mm ± 1.09 mm (95% CI: 0.99–1.79, P < 0.001), whereas mandibular alveolar crest width showed a minimal increase of 0.38 mm ± 0.75 mm (95% CI: 0.10–0.66, P = 0.008). No significant changes were observed in apical basal bone width in either arch. Conclusion The findings suggest that CEA may expand maxillary and mandibular arches in mixed dentition children with maxillary transverse deficiency. The maxillary expansion effect primarily involves dental movement and adaptive dentoalveolar change, without significant deep basal bone changes. In the mandible, significant dental expansion was observed at the cusp level, while the alveolar bone changes were minimal and should be interpreted cautiously. These findings provide preliminary CBCT-based evidence for the transverse expansion effects of CEA in mixed dentition children. Clinical trial registration Not applicable. This is a retrospective, anonymous observational study without prospective intervention or a clinical trial protocol.