Bipolar disorder is known to be subject to maternal transmission. Mitochondrial DNA has been suggested as playing a role in the illness. NDUFV2, located on 18p11.31-p11.2, encodes an important subunit of mitochondrial NADH (complex I). Previous studies have reported the association of NDUFV2 with bipolar disorder in the Japanese and Caucasian populations. Whether it is also a susceptible gene in the Chinese population is unknown. To study the role of NDUFV2 in bipolar disorder in the Chinese population, 506 unrelated bipolar patients and 507 unrelated controls of Chinese Han origin were recruited. Six SNPs (rs11661859, rs6506640, rs1156044, rs4148965, rs906807, rs977581) were genotyped using either TaqMan® technology or direct sequencing. The haplotype consisting of rs6506640 (−342G > A) and rs906807 (86C > T) was found to be associated with bipolar disorder (global p = 0.012 before corrected, p = 0.030 after 10,000 permutations; individual p (A–T of rs6506640–rs906807) = 0.014 after 100,000 permutations (p = 0.0065 before corrected). The genotype frequency of rs906807 differed between bipolar female patients and female controls (p = 0.012, uncorrected). No other individual associations of SNPs with bipolar were detected. Our study indicated that the regions spanning from the promoter to the exon 2 may contain susceptible polymorphisms which predispose to bipolar disorder.