Copy number variations (CNVs) in chromosome 16p11.2 are not rare. 16p11.2 microdeletion is among the most commonly known genetic etiologies of overweightness, autism spectrum disorder (ASD), and related neurodevelopmental disorders. We report the prenatal diagnosis and genetic counseling of three cases with inherited 16p11.2 microdeletions. In these families, mother/father and fetus have the same microdeletion. Following the use of molecular genetic techniques including array-based methods, the number of reported cases has rapidly increased. A combination of prenatal three-dimensional ultrasound, karyotype analysis, chromosomal microarray analysis (CMA), copy number variation sequencing (CNV-seq), whole-exome sequencing (WES), and genetic counseling is helpful for the prenatal diagnosis of chromosomal microdeletions/microduplications.