OBJECTIVE: We aimed to explore the value of chromosome microarray analysis (CMA) and karyotyping in fetuses with a high risk for Down syndrome (DS) by serological screening and prenatal cell-free DNA(cfDNA) screening in Southwest China. METHODS: We performed CMA and karyotype in 3028 pregnant women at high risk of DS. RESULTS: Among 2,830 individuals identified as high-risk through serological screening for DS, 280 (9.89%) returned positive results. Subsequent karyotyping confirmed 51 cases of DS, 13 cases of sex chromosome aneuploidy, and 11 cases of trisomy 18. Moreover, CMA revealed 45 cases of pathogenic/likely pathogenic copy number -variations (p/lpCNVs), 128 cases of uncertain significance(VOUS), and 32 cases of regions of homozygosity(ROH), with a 13.04% (205/280) increase in CMA yield compared to the karyotype analysis. Among 227 who had a high risk of prenatal cfDNA screening for DS, 181 (79.74%) exhibited positive results, including 179 cases with DS. CONCLUSION: Serological screening cannot be replaced by prenatal cfDNA screening. CMA, combined with karyotyping, has a high diagnostic value for DS and should be promoted.