Objective To analyze prenatal diagnosis, genetic counseling and follow-up of five fetuses with isodicentric Y chromosomes and to provide reference for the clinical treatment. Methods From January 2018 to August 2022, 7 347 pregnant women with prenatal diagnostic indications were selected, and fetal amniotic fluid was detected by conventional G-banding karyotype and chromosomal microarray analysis (CMA) simultaneously, and then verified by fluorescence in situ hybridization (FISH). Subsequently, parental karyotypes were analyzed. After genetic counseling, pregnant outcomes were followed up. Results Five fetuses with de novo idic(Y) were detected and all of these Y chromosomes had the same breakpoint in Yq11.2. Among them, four fetuses (cases 2~5) presented with a mosaic 45, X karyotype except the fetus of case 1. Prenatal ultrasonography indicated that all five fetuses were male and no obvious structural abnormalities were found in the other four fetuses except for case 1 with possible bilateral clubfeet. After personalized genetic counseling combined with the ultrasonography results, cases 1~2 chose to continue the pregnancy while cases 3~5 terminated the pregnancy. The child of case 1 was followed up to four years old. The surgical effect of strephenopodia was good, and the mild developmental retardation was improved after rehabilitation training. The child of case 2 was followed up to 2 years old, and no abnormal phenotype was found yet. Case 3 had been pregnant again and had given birth to a healthy baby girl while cases 4 and 5 were still in preparation for pregnancy. Conclusions The combined application of cellular and molecular genetic techniques is helpful for the prenatal diagnosis of the fetuses with idic(Y). Reasonable genetic counseling and long-term follow-up can provide an important reference for subsequent clinical diagnosis and treatment.