Background: PAHs exposure had been reported to be a risk factor of mtDNAcn in our early study. However, the effect of metabolic enzymes’ genetic polymorphisms on mtDNAcn in PAHs-Exposure workers has not been fully evaluated.Methods: We investigated the effects of metabolic enzymes’ genetic polymorphisms on mtDNAcn among 544 coke oven workers and 238 office staffs. The mtDNAcn of peripheral blood leukocytes was measured using Real-time quantitative polymerase chain reaction method. Polymerase chain reaction and restriction fragment length was used to detect five polymorphisms in GSTT1, GSTM1, GSTP1 rs1695, CYP2E1 rs6413432, and CYP2E1 rs3813867.Results: The mtDNAcn in peripheral blood leukocytes was significantly lower in the exposure group than that in the control group (P < 0.001). The 1-OHPYR had an increasing trend with the genotypes AA→AG→GG of GSTP1 rs1695 in the control group. Generalized linear model indicated that the influencing factors of mtDNAcn were PAHs-exposure [b(95% CI) = -0.420 (-0.469, -0.372), P < 0.001], male [β(95% CI) = -0.058 (-0.103, -0.012), P = 0.013] ,and AA genotype for GSTP1 rs1695 [β(95% CI) = -0.051 (-0.095, -0.008), P = 0.020].Conclusions: The male was susceptibility to PAHs exposure. The AA genotype of GSTP1 rs1695 may influence the toxicity of PAHs and associated with the decreased of mtDNAcn.