INTRODUCTION: Transient infantile hypertriglyceridemia (HTGTI) is a rare autosomal recessive disease. At present, only 20 cases of HTGTI have been reported worldwide. Hence, it is necessary to further assess the phenotypic and genetic variation spectra of HTGTI. CASE PRESENTATION: A 10-month-old male infant was diagnosed with hypertriglyceridemia, hepatomegaly, liver injury, fasting hypoglycemia, and insulin resistance. Trio-whole exome sequencing (trio-WES) was performed on the patient and his parents. Bioinformatics software was used to analyze the suspected genes and potential pathogenicity of the resulting mutant proteins. The results of trio-WES demonstrated that the patient was homozygous for a novel mutation in the GPD1 gene (NM_005276.3; c.805C>T/p.Arg269Trp), whereas his parents were heterozygous for the same mutation. Bioinformatics prediction results demonstrated that the mutation might affect the protein function, and crystal simulation results showed that the mutation might affect the protein-binding ability of the enzyme. CONCLUSION: Our results indicated that the novel homozygous mutation in GPD1 could be the pathogenic factor in the patient. Our report highlights the value of genome sequencing in the diagnosis of infant liver disease with low phenotypic heterogeneity.