Abstract: 　Objective　To explore the value of chromosome microarray analysis (CMA) in genetic-etiological diagnosis of congenital multiple malformations in neonates. Method　Chromosome G-banding karyotype analysis and CMA analysis were performed in 100 children. Results　The most common clinical manifestations of 100 children were cardiovascular malformation combined with other system deformities, accounting for 69%. G-banding karyotype analysis showed that 21 children (21%) had chromosomal abnormalities, Among whom there were 9 children with numerical abnormality of autosomal chromosomes, 2 with numerical abnormality of sex chromosomes and 10 with structural abnormality of autosomal chromosomes. Gene copy number variations (CNVs) were performed by CMA analysis in 79 children with normal chromosome karyotype. Seven cases were found to have CNVs, including 4 cases of pathogenic CNVs, 2 cases of uncertain CNVs and one case of clinically unknown CNVs. Conclusion　CMA has the advantages of high resolution and wide coverage. It can find the deletion and repetition from the submicrostructures, so as to diagnose the genetic etiology of congenital multiple malformations in neonates.