Abnormalities in mitochondrial complex I, which is responsible for controlling mitochondrial function, have been implicated in a variety of diseases associated with mitochondrial dysfunction, potentially including schizophrenia. The NADH dehydrogenase Fe-S protein 1 (NDUFS1) is the largest subunit of complex I. To explore whether the encoding NDUFS1 gene confers susceptibility to schizophrenia or is associated with the severity of typical symptoms of schizophrenia, we recruited 519 stable schizophrenia patients receiving clozapine treatment and 594 healthy controls for genotyping to investigate the association of four selected tagging single-nucleotide polymorphisms (SNPs) of NDUFS1 and both schizophrenia risk and symptom severity. The severity of psychotic symptoms was evaluated using the Positive and Negative Syndrome Scale and then tested for association with the four SNPs. The SNP rs1044120 showed significant association with schizophrenia (adjusted P=0.032). The frequency of the G allele of rs1044120 was significantly higher in patients than among the healthy controls (adjusted P=0.008). Stratification by sex revealed a significant association between the rs1044120 polymorphism and schizophrenia among males (adjusted P=0.036 and 0.008 in genotypic and allelic comparisons, respectively). We also observed a significant difference in the negative symptom scores among the three genotypes among these males (adjusted P=0.036). Post hoc comparisons showed that rs1044120 G/G carriers had higher negative symptom scores than those with G/T and T/T carriers (raw P=0.035 and 0.005, respectively). Our findings suggest that NDUFS1 may confer susceptibility to schizophrenia in male subjects, acting as a causative factor for the severity of negative symptoms in schizophrenia.