Transfemoral device occlusion and minimally invasive surgical repair are performed for doubly committed subarterial ventricular septal defect (dcVSD) to reduce the invasiveness of the conventional surgical repair through a median sternotomy. However, few studies have compared them in terms of effectiveness and cost. Inpatients with isolated dcVSD who had undergone transfemoral device occlusion or minimally invasive surgical repair from January 2011 to June 2014 were reviewed for a comparative investigation between the two procedures. Procedure success was achieved in 36 transfemoral (75 %) and in 36 surgical (100 %) procedures (p = 0.001). Transfemoral patients were older, with a VSD size similar to that of surgical patients (14.5 ± 11.7 vs 4.4 ± 2.9 years, p < 0.001; 4.5 ± 1.5 vs 4.4 ± 1.3 mm, p = 0.577, respectively). No significant difference was observed in complication rates between the two treatment groups (p = 1). No large residual shunt was observed. Small residual shunt was noted in two transfemoral patients and four surgical patients (p = 0.674). All these small residual shunts closed spontaneously during follow-up. The surgical repair costs 26 % less than the device occlusion (Yuan 22063.2 ± 343.9 vs Yuan 29970.1 ± 1335.2, p < 0.001), where most of the cost was attributed to the occluder in the amount of Yuan 19,500. Compared with device occlusion, minimally invasive surgical repair can provide superior efficacy and comparable complication rates. In addition, it is 26 % cheaper than device occlusion. In low-income countries where healthcare resources are limited, medical resources must be judiciously allocated to the treatment that allows for effective treatment of the largest number of patients.