Apical multiple muscular ventricular septal defects (VSDs) are difficult to visualize, and closing these VSDs is technically troublesome. For these reasons, the surgical outcome of the lesion is unsatisfactory. Some surgical techniques have been reported to improve the outcome, but they are not definite. We present a case with atrial septal defect, multiple muscular and perimembranous VSDs, and pulmonary hypertension due to high pulmonary blood flow. In the first operation during the infantile period, the patient received closure of the perimembranous and muscular VSD through the right atrium and atrial septal defect closure. However, postoperative pulmonary blood flow was not decreased compared with that of before the operation, and pulmonary hypertension was also not improved. In addition to these lesions, tricuspid valve insufficiency was also observed after the operation. Postoperative computed tomography showed channels of apical muscular VSDs in the apex of the right ventricle. In the second operation, exclusion of apex muscular VSDs using the felt sandwich technique and tricuspid valve repair were performed. After closing multiple muscular VSDs during the operation, pulmonary blood flow was significantly decreased, and pulmonary hypertension was improved as well. After the second operation, postoperative echocardiography and catheter examination showed decreased VSD shunt and pulmonary blood flow, resulting in improved pulmonary hypertension.