Objective To explore the copy number variants (CNVs) in case of fetal duodenal obstruction (DO) and assess the associated prenatal findings and postnatal outcomes. Materials and methods This retrospective study reviewed 51 fetuses with DO and the findings of chromosomal microarray analysis (CMA) used as a first‐tier test in our institution between January 2014 and May 2019. Results The frequency of pathogenic aberrations in fetuses with DO was 15.7% (8/51), including 9.8% (5/51) pathogenic CNVs. Three fetuses with isolated DO each had a deletion on chromosome 13q, one fetus had duplication at 1q43q44, and one had microduplication at 17q12. No significant differences in pathogenic CNVs were observed between isolated DO and DO plus additional anomalies (4/42, 9.5% vs 1/9, 11.1%, P = .89). Of the 51 fetuses with DO, 11 pregnancies were terminated, and eight fetuses had chromosomal abnormalities; one pregnancy ended with intrauterine death, and there were 39 live births. Neonatal outcomes were available for 31 fetuses, and no neonatal deaths occurred after surgery. Conclusions Our cohort study demonstrated the value of CMA in fetuses with DO, suggesting that CNVs may underly genetic etiologies that should be considered in the diagnostic evaluation of DO. We think CMA should be recommended in case of DO.