Genomic diseases caused by pathogenic copy number variations (pCNVs) are a group of important causes for birth defects. At present, the methods used to detect CNV mainly include chromosomal microarray analysis (CMA) and copy number variation sequencing (CNV-seq) based on next generation sequencing (NGS). In recent years, CNV detection technology has been widely used in the field of prenatal diagnosis. To standardize the clinical application of such technologies, the authors have formulated a guideline for the application of CNV testing in prenatal diagnosis, which includes the basic requirement, scope of application, clinical testing and consultation, procedure of CNV analysis in prenatal diagnosis, with an aim to better serve the patients.