Background: Emerging studies suggest that low‐coverage massively parallel copy number variation sequencing (CNV-seq) provide advantage in detecting low-level mosaicism compared with chromosomal microarray analysis (CMA). However, a prospective back-to-back comparison evaluating accuracy, efficacy, and incremental yield of CNV-seq compared with CMA is warranted. Methods: A total of 72 mosaicism cases identified by karyotyping or CMA were recruited in this study, and 67 samples (40 sex chromosome aneuploidy, 22 autosomal aneuploidy and 5 submicroscopic CNVs) were eventually analyzed by CNV-seq. Results: CNV-seq not only identified all 43 chromsomal aneuploidies or submicroscopic CNVs detected by CMA, but also provided a 34.88% (15/43) increased yield compared with CMA. Besides, the level of mosaicism defined by CNV-seq range from 6% to 92%. Conclusion: In the context of prenatal diagnosis, CNV-seq identified additional and clinically significant information with enhanced resolution and increased sensitivity of detecting mosaicism as compared with the CMA platform we used. This study provides strong evidence for applying CNV-seq as an alternative prenatal diagnostic test.