Abstract The concomitant occurrence of 8q duplication and 13q deletion is the first to be detected by noninvasive prenatal testing (NIPT) to date. Through case analysis, we could provide a clinical approach to pregnant women with chromosomal abnormalities revealed by NIPT. The combination of traditional karyotype and copy number variation sequencing (CNV‐seq) could better locate the abnormal chromosomal region and further identify the source of fetal chromosomal abnormalities. Simultaneously, we evaluated the fetal morphology by ultrasound examination. The karyotype of the fetus was 46,XY,der(13)t(8;13)(q22;q32)mat and CNV‐seq results showed that there was an approximately 45.26‐Mb duplication in 8q22.2‐q24.3 (101040001–146 300 000) and an approximately 9.54‐Mb deletion in 13q33.2‐q34 (105560001–115 100 000). Prenatal ultrasound revealed the fetal structural abnormalities presented with hypoplasia of the cerebellar vermis, a flat nose, echogenic bowel and absent gallbladder. Herein, we consider that combination detection of traditional karyotyping, CNV‐seq and ultrasonography provides a valuable method for pregnant women with abnormal NIPT.