Objective To improve the understanding of the clinical phenotype and genotype of mitochondrial complex I deficiency nuclear type 20 (MC 1 DN 20 ). Methods The clinical data of mitochondrial complex I deficiency nuclear type 20 in a child was analyzed retrospectively and the related literature was reviewed. Results A boy was born with poor spirit and reaction, refractory metabolic acidosis, hyperlactacidemia and liver enlargement. A maternal splicing mutation of c.1278 +1 G>A and a paternal missense mutation of c. 895 A>T were found in ACAD 9 gene by whole exome gene sequencing. No significant mitochondrial gene variation and large fragment variation was found in the second-generation sequencing of mitochondrial gene and multiplex ligation-dependent probe amplification. Conclusion It was found that the c.1278 + 1 G>A splicing mutation and the c.895 A>T missense mutation of the new mitochondrial nuclear gene ACAD9 leads to MC1 DN 20 .