Infantile scimitar syndrome is a rare type of partial pulmonary venous return that is sometimes complicated by severe pulmonary hypertension, which has a poor prognosis. As the genetic background of Scimitar syndrome remains unclear, we report a case of an infant with scimitar syndrome that was analyzed using a chromosomal microarray. Fetal echocardiography revealed an abnormal return of the entire right pulmonary vein to the inferior vena cava. The patient presented with abnormal physical features and a history of atrial septal defects, multiple muscular ventricular septal defects, chronic pleural chylothorax, and hypertrophic pyloric stenosis. The patient died at the age of 3 months despite receiving multidisciplinary treatment with nitric oxide and a pulmonary vasodilator for severe pulmonary hypertension. Chromosomal microarray analysis revealed a copy number loss of 3p.26.1–26.3 (6.5 Mb), a copy number gain of 12q23.2–24.3 (30.8 Mb), and a determined karyotype of 46, XY, der (3) t (3;12) (p26.1;q23.2), arr [grch37] 3p26.1p26.3(62,199_6,541,934) x1,12q23.2q24.3(102,869,918_133,747,247) x3. We report a case of multiple malformations, including Scimitar syndrome and severe pulmonary hypertension with a novel unbalanced translocation involving a 3p26.1–26.3 microdeletion and a 12q23.2–24.3 microduplication. The relationship between unbalanced translocations and the phenotype and prognosis of scimitar syndrome requires further investigation.