Although septal myectomy is the preferred treatment for medication-refractory hypertrophic obstructive cardiomyopathy (HOCM), the procedure remains subjective. A preoperative planning procedure is proposed using computational fluid dynamics simulations and shape optimization to assist in the objective assessment of the adequacy of the resection. 3 patients with HOCM were chosen for the application of the proposed procedure. The geometries of the preoperative left ventricular outflow tract (LVOT) of patients in the systolic phase were reconstructed from medical images. Computaional fluid dynamics (CFD) simulations were performed to assess hemodynamics within LVOT. Sensitivity analysis was performed to determine the resection extent on the septal wall, and the depth of the resection was optimized to relieve LVOT obstruction while minimizing damage to the septum. The optimized resection was then transferred from systole to diastole to provide surgeons with instructive guidance for septal myectomy. Comparison between preoperative and postoperative hemodynamics showed an evident improvement with respect to the pressure gradient throughout the LVOT. The resected myocardium in the diastolic phase is more extended and thinner than its state in the systolic phase. The proposed preoperative planning procedure may be a viable addition to the current preoperative assessment of patients with HOCM.