Congenital heart defect (CHD) is one of the most common birth defects in China, while pulmonary atresia with intact ventricular septum (PA–IVS) is the life-threatening form of CHD. Numerous previous studies revealed that rare copy number variants (CNVs) play important roles in CHD, but little is known about the prevalence and role of rare CNVs in PA–IVS. In this study, we conducted a genome-wide scanning of rare CNVs in an unselected cohort consisted of 54 Chinese patients with PA–IVS and 20 patients with pulmonary atresia with ventricular septal defect (PA–VSD). CNVs were identified in 6/20 PA–VSD patients (30%), and three of these CNVs (15%) were considered potentially pathogenic. Two pathogenic CNVs occurred at a known CHD locus (22q11.2) and one likely pathogenic deletion located at 13q12.12. However, no rare CNVs were detected in patients with PA–IVS. Potentially pathogenic CNVs were more enriched in PA–VSD patients than in PA–IVS patients (p = 0.018). No rare CNVs were detected in patients with PA–IVS in our study. PA/IVS might be different from PA/VSD in terms of genetics as well as anatomy.