Purpose The present study aimed to evaluate the genetic diagnostic yield and accuracy of exome sequencing in Chinese patients with split hand–foot malformation (SHFM), a severe heterogeneous congenital anomaly characterized by hypodevelopment of the central ray of the hands and feet.Methods A cohort of seven families and five sporadic patients with SHFM was investigated. Genomic DNA was prepared from the peripheral blood of affected as well as unaffected individuals. Whole exome sequencing (WES) was performed to identify the pathogenic mutations. Array-based comparative genomic hybridization (aCGH), CytoScan, quantitative polymerase chain reaction (qPCR), and Sanger sequencing were performed to validate the ifndings of WES. WES data of an additional cohort of 24 patients with non-SHFM congenital hand anomalies were analyzed as the control. Results Pathogenic variants of TP63, c.G956A p.R319H, and c.T602A:p.L201H, were identiifed in two families by WES. In the remaining patients, copy number analysis of the WES data by XHMM software identiifed pathogenic 10q 24 duplication in ifve individuals from three families, which was further validated via CytoScan and qPCR; however, WES could not detect duplication in 10q24 in an additional cohort of 24 individuals with non-SHFM congenital hand anomaly. Importantly, qPCR analysis of the 10q24 region copy number revealed a definite consistency with WES data in all individuals. Genotype–phenotype analysis did not present any unique feature that could differentiate between the families with TP63 mutation and 10q24 duplication. Conclusions Our study demonstrated that WES is an accurate and sensitive method to detect the pathogenic 10q24 duplication. Collectively, with TP63 mutation, a single WES testing could yield a diagnosis rate of about 40％ (5/12) for the SHFM patients, at least in our cohort. As the genotype–phenotype correlation remains unclear, WES could be used as a cost-effective method for the genetic diagnosis of SHFM.