Objective　To investigate the clinical phenotype and genetic characteristics of loss of heterozygosity (LOH) in chromosome fragment 3p25.3p25.2. Method　The clinical data, clinical phenotype and molecular genetic characteristics of LOH in chromosome fragment 3p25.3p25.2 in a child were analyzed retrospectively. Results　A boy, aged 1 year and 4 months old, suffered from intrauterine growth retardation, severe short stature, overall growth retardation, language retardation and special face with multiple malformations (microcephaly, head appearance deformity, small mandible, long philtrum, low ear position, bilateral preauricular fistulas, etc.). He also had congenital duodenal atresia, intestinal malrotation, congenital heart disease, cryptorchidism, glans exposure, hypotonia, feeding difficulties in infancy, sleep disorders and hypothyroidism. Chromosome karyotype of the child showed 46, XY. Chromosomal microarray analysis results demonstrated a 3327 kb heterozygous deletion in 3p25.3p25.2, a total of 39 gene deletions. Conclusion　The loss of heterozygosity of 3327 kb in 3p25.3p25.2 region resulted in the deletion of SETD5, VHL, and FANCD2 genes, which led to the clinical phenotype of this child.