Perventricular device occlusion and minimally invasive surgical repair for perimembranous ventricular septal defect (pmVSD) are two typical methods to reduce the invasiveness of the conventional operation through median sternotomy. However, few comparative studies have been made between them in terms of effectiveness and cost. A review was made of the inpatients with isolated pmVSD, who had undergone perventricular device occlusion or minimally invasive surgical repair from June 2011 and January 2013 for a comparative investigation between the two procedures. The two treatment groups had similar baseline characteristics. Procedural success was achieved in 163 (94.8 %) of the perventricular and 137 (98.6 %) of the surgical (P = 0.136). Major complications occurred in 2 (1.2 %) of the perventricular and 4 (2.9 %) of the surgical (P = 0.497), and minor complications, in 57 (33 %) of the percutaneous and 49 (35.2 %) of the surgical (P = 0.696). In cost, the surgical repair was 30.5 % cheaper than the device occlusion (Yuan 20139 ± 3760 vs. 28970 ± 3343, P < 0.001), where most of the cost was attributed to the occluder in the amount of Yuan 19,500. Compared with perventricular device closure, minimally invasive surgical repair can provide comparable efficacy and complication rates, without the potential for developing atrioventricular block at long-term follow-up. In addition, it is 30.5 % cheaper than hybrid procedure. In the low-income countries where health-care resources are limited the medical resources must be judiciously allocated to the treatment that allows for effective treatment of the largest number of patients.