Objective To investigate the diagnosis of a case with 7p15.3p22.1 microdeletion by applying array-based comparative genomic hybridization (array-CGH) and to analyze the relationship between the clinical manifestations and 7p15.3p22.1 microdeletion. Method Array-CGH technique was used to detect genomic copy number variations (CNVs) in an infant with normal karyotype after conventional chromosomal karyotyping. Results Array-CGH detected 7p15.3p22.1 deletion (chr7: 6777262-23981753), which was confirmed as pathogenic CNV after comparative analysis with database. Conclusion Array-CGH could serve as a useful complement for G-banding to be used in the clinical cytogenetic diagnosis.