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Background Proton therapy, with its superior dose distribution, has emerged as a promising radiotherapy (RT) technique. This study evaluates the clinical benefits of proton therapy in reducing treatment-related toxicities in breast cancer patients undergoing radiotherapy. Methods A retrospective analysis was performed using the Chang Gung Research Database, identifying 8189 breast cancer patients treated with adjuvant radiotherapy from 2012 to 2022. Patients received either intensity-modulated proton therapy (IMPT, n  = 501) or photon-based IMRT/VMAT ( n  = 7688). Propensity score weighting was applied to adjust for baseline differences. The clinical outcomes photon and proton therapy were investigated, with a particular focus on radiation-induced toxicities including dermatitis, pulmonary changes, and cardiac events. In addition, N-terminal pro-brain natriuretic peptide (NT-proBNP), a biomarker of cardiac stress, was prospectively assessed in a subset of patients to assess subclinical cardiac injury between 2023 and 2024. Results Compared with photon therapy, proton therapy significantly reduced the incidence of radiographic pulmonary changes and subclinical cardiac biomarker elevations, while maintaining comparable loco-regional control and overall survival. Proton therapy significantly reduced the incidence of radiographic pulmonary changes (5.8% vs. 10.0%, p  = 0.02; HR: 0.64, 95% CI 0.44–0.93) and grade 2 radiation dermatitis (13.4% vs. 20.9%, p  < 0.001), though grade ≥ 1 skin toxicity was more common with IMPT (82% vs. 57.1%). Among left-sided patients, photon RT resulted in significantly greater NT-proBNP elevation post-treatment compared to proton therapy (mean ratio: 1.16 vs. 0.95, p  = 0.0099), suggesting more subclinical cardiac stress. However, no significant difference in clinically evident cardiac events was noted between the groups during the follow-up period. Conclusions Proton therapy is associated with reduced radiation-induced pulmonary toxicity and moderate dermatitis, while achieving comparable oncologic outcomes to photon therapy. The lower NT-proBNP elevation suggests potential cardiac sparing, although longer follow-up is needed to confirm clinically meaningful cardiac benefits. These findings highlight the potential role of proton therapy in mitigating treatment-related toxicities in breast cancer patients at elevated risk for cardiopulmonary complications.