This study aimed to compare the efficacy and safety of the classic Morrow septal myectomy with the modified procedure in treating hypertrophic obstructive cardiomyopathy (HOCM). A retrospective study was conducted to compare the outcomes of classic with modified Morrow septal myectomy in 42 patients treated from January 2005 to July 2011. Preoperative and postoperative ventricular septal thickness, left ventricular (LV) outflow tract velocity and gradient were measured echocardiographically. In both groups, the ventricular septal thickness, LV outflow tract velocity, and LV outflow tract gradient were significantly decreased after the operation. The modified Morrow procedure group, however, showed significantly greater reduction in these echocardiographic parameters than the classic procedure group. All patients in the modified procedure group were asymptomatic postoperatively with a postoperative transvalvular pressure gradient <30 mm Hg. In the classic procedure group, only 14 (87.5%) patients, however, were asymptomatic postoperatively with a postoperative transvalvular pressure gradient <30 mm Hg, and 2 patients still had severe LV outflow obstruction postoperatively. The modified Morrow septal myectomy is safe and effective in treating HOCM patients, and is superior to the classic procedure in reducing the LV outflow tract gradient and velocity, restoring normal anatomic atrioventricular size, and alleviating symptoms associated with HOCM.