Background: Right ventricular involvement in hypertrophic cardiomyopathy is uncommon. This study aimed to evaluate clinical outcomes of the modified septal myectomy in patients diagnosed with biventricular hypertrophic cardiomyopathy (BHCM), a subject seldom explored in the literature. Methods: We conducted a retrospective cohort study from January 2019 to January 2023, enrolling 12 patients with BHCM. Each patient underwent a modified septal myectomy and was followed postoperatively. Clinical data and echocardiographic parameters, including the ventricular outflow tract peak pressure gradient and maximum interventricular septum thickness, were collected and analyzed. Results: The study cohort had a median age of 43.0 (interquartile range 14.5–63.0) years at surgery, with four patients (33.3%) being children. Two patients (16.7%) previously underwent percutaneous transluminal septal myocardial ablation. Surgical relief of biventricular outflow tract obstruction (BVOTO) was achieved in five patients (41.7%), aside from those managed solely for left ventricular outflow tract obstruction. In five instances, three-dimensional (3D) printing technology assisted in surgical planning. The postoperative interventricular septum thickness was significantly reduced (21.0 mm preoperative vs. 14.5 mm postoperative, p 0.001), effectively eliminating residual ventricular outflow tract obstruction. There were no severe complications, such as septal perforation or third-degree atrioventricular block. During a mean follow up of 21.2 \pm 15.3 months, no sudden deaths, residual outflow tract obstruction, permanent pacemaker implantation, recurrent systolic anterior motion, or reoperations were reported. Conclusions: Our findings affirm that the modified septal myectomy remains the gold standard treatment for BHCM, improving patient symptoms and quality of life. BVOTO relief can be safely and effectively achieved through septal myectomy via transaortic and pulmonary valve approaches in selected patients. For intricate cases, the application of 3D printing technology as a preoperative planning tool is advised to optimize surgical precision and safety.