To detect potential mutation of NFU1 gene in a Chinese family affected with multiple mitochondrial dysfunction syndrome (MMDS). For a mother with two children died of MMDS, next-generation sequencing (NGS) was used to scan her exome. Suspected mutation was validated with PCR and Sanger sequencing. Potential mutation of exons 1 to 8 and flanking regions of the NFU1 gene was also detected in the father by PCR and Sanger sequencing. A novel deletional mutation c.90delC(p.Tyr30Ter) of the NFU1 gene was found in the mother, while the father was found to have carried a heterozygous c.572A>T (p.Asp191Val) mutation. The same mutations were not found among 100 healthy controls. The novel mutations c.90delC (p.Tyr30Ter) and c.572A>T (p.Asp191Val) of the NFU1 gene probably underlie the pathogenesis of MMDS in our case. Combined NGS and Sanger sequencing may provide efficient and accurate diagnosis for this disease.