Objective To compare the efficacy of a new precision surgical system and traditional surgical instruments in the treatment of hypertrophic obstructive cardiomyopathy (HOCM).Methods Eight 4-month-old male Guangxi Bama miniature pigs were used to prepare HOCM models, and were randomly divided into control group (n＝4) and experimental group (n＝4). The pigs in both groups underwent modified extended Morrow procedure by the same team. The ventricular septal hypertrophy tissues were removed in the control group with traditional surgical instruments such as sickle blade, while in the experimental group with a new precision surgical system. Echocardiography was performed by the same physician 24 h before and 72 h after surgery. Anteroposterior diameter of the left atrium, interventricular septal thickness, left ventricular end-diastolic diameter, mean pressure difference of left ventricular outflow tract (LVOT), left ventricular ejection fraction, systolic anterior motion (SAM) of the mitral valve, and mitral valve regurgitation were measured. Serum N-terminal pro-brain natriuretic peptide (NT-proBNP) level was detected by chemiluminescence method.Results The extracorporeal circulation time and aortic occlusion time in the experimental group were significantly shorter than those in the control group (both P < 0.05). The postoperative interventricular septal thickness, mean pressure difference of LVOT, anteroposterior diameter of left atrium, left ventricular ejection fraction, mitral valve regurgitation, and serum NT-proBNP level were significantly lower than preoperative ones in both groups (all P < 0.05). The postoperative interventricular septal thickness, mean pressure difference of LVOT and serum NT-proBNP level of the experimental group were significantly lower than those of the control group (all P < 0.05). All HOCM pigs survived 72 h after surgery, aortic valve injury was detected in 1 HOCM pig in each group, and there were no left bundle branch block or iatrogenic ventricular septal perforation.Conclusion Compared with the traditional surgical instruments, the new HOCM precision surgical system can accurately remove the ventricular septal hypertrophy tissues, significantly shorten the operative time and improve the short-term treatment outcome without increasing the early postoperative complications or mortality.