Background: A modified Morrow septal myectomy (MMSM) is one of the main treatment methods for obstructive hypertrophic cardiomyopathy (OHCM). Our aim was to study the impact of MMSM on the risk of AF and stroke in OHCM patients. Methods and Results: From 1 January 2014 to 31 December 2020, 6426 patients with obstructive HCM (OHCM) were selected from the Beijing Municipal Health Commission Information Center (BMHCIC) datasets (mean age: 54.3 years; 43.8% female). After propensity score matching, 3780 patients were selected, including 1890 who received MMSM (Group 1) and 1890 who did not receive any surgery (Group 2). During a median of 0.8 (interquartile range [IQR]: 0.1, 2.7) years of follow-up after discharge from the hospital, stroke risk was lower in Group 1 compared to Group 2 (aHR: 0.4, 95%CI: 0.2-0.6, p < 0.001), and the results were further confirmed by Kaplan-Meier analyses (p < 0.001). There was no statistically significant difference in the risk of AF (aHR: 1.0, 95%CI: 0.7-1.5, p = 0.991). The risk of AF decreased in the first 6 years since receiving MMSM and then sharply increased beyond 6 years after MMSM according to Kaplan-Meier analyses. Conclusions: MMSM is associated with a decreased risk of stroke in OHCM patients. The risk of AF decreased in the first 6 years since receiving MMSM and then sharply increased beyond 6 years after MMSM.