This study aims to investigate the risk factors of in-hospital postoperative atrial fibrillation (POAF) and the impact of POAF on the clinical outcome in hypertrophic cardiomyopathy (HCM) patients who underwent myectomy. Data from a total of 494 obstructive HCM patients, who had undergone preoperative cardiac magnetic resonance (CMR) testing and who underwent myectomy at Fuwai Hospital from June 2011 to June 2016, were collected. Multivariate logistic regression analysis showed that old age (odds ratio [OR], 4.326; 95% confidence interval [CI], 2.248-8.325; p <0.001), maximal left atrium volume (LAV) (OR, 1.137; 95% CI, 1.075-1.202; p <0.001), and hypertension (OR, 2.754; 95% CI, 1.262-6.007; p = 0.011) were associated with the incidence of POAF. In the patients without preoperative AF, Cox regression analysis demonstrated that POAF (p = 0.002), decreased left atrium (LA) ejection fraction (LAEF) (p = 0.036), concomitant procedure (p = 0.039), and postoperative residual moderate or severe mitral valve regurgitation (p = 0.030) were independent predictors of composite cardiovascular events. POAF indicated a poorer clinical outcome after myectomy for obstructive HCM patients, which was similar to those with preoperative AF. Elevated LAV was independently related to POAF onset in HCM patients who underwent myectomy.