Objective To investigate the clinical phenotype, genetic counseling, pregnancy outcomes, and long-term developmental outcomes of fetuses with 1q21.1 microdeletion/ microduplication syndrome, and to provide a comprehensive clinical picture of fetuses with this copy number variation to inform clinical decision-making. Methods A retrospective analysis was conducted of pregnant women from January 2017 to December 2022. Results 39 cases of 1q21.1 microdeletion/microduplication syndrome fetuses were identified, with a detection rate of 0.16% (39/24,240). The size range of the copy number variation segments was 0.24 Mb to 62.34 Mb, with 22 cases (56.4%) being 1q21.1 microdeletions and 17 cases (43.6%) being 1q21.1 microduplications. Among the 22 cases of 1q21.1 microdeletion fetuses, 10 had prenatal ultrasound abnormalities (10/22, 45.6%), 4 had high-risk non-invasive/serological screening results (4/22, 18.2% ), 5 cases were of advanced maternal age (5/22, 22.7%), and 3 cases had a history of adverse pregnancy outcomes (3/22, 13.6%); among the deletion cases, 6 underwent parental origin testing, revealing 2 de novo mutations, 3 paternal origin, and 1 maternal. Among the 17 cases of 1q21.1 microduplication fetuses, 8 had prenatal ultrasound abnormalities (8/17, 45.6%), 4 had high-risk non-invasive/serological screening results (5/17, 29.4%), 5 were of advanced maternal age (2/17, 11.8%), and 3 had a history of adverse pregnancy outcomes (3/17, 17.6%); among the repeat cases, only 1 case showed a de novo mutation after parental lineage tracing. Conclusion 1q21.1 microdeletions/microduplications exhibit diverse manifestations during fetal development. CNV-seq technology holds significant value for detecting fetal cases of chromosomal microdeletion/microduplication syndromes, including 1q21.1.