Background Hypertrophic cardiomyopathy (HCM) significantly increases the risk of new-onset atrial fibrillation (AF) through distinct pathogenic mechanisms. This study develops a machine learning (ML) model to improve AF prediction in patients with HCM and investigates electrophysiological abnormalities and non-traditional factors as preclinical predictors. The findings aim to inform early warning systems and precision management strategies for AF in this patient cohort. Methods This retrospectiv