We aimed to evaluate the association between polycyclic aromatic hydrocarbons (PAHs)-related microRNAs (miRNAs) and heart rate variability indices in coke oven workers. We recruited 365 male coke oven workers and measured urinary PAH metabolites by gas chromatography-mass spectrometry. Five heart rate variability indices were measured using three-channel Holter monitor. Six miRNAs were detected by TaqMan miRNA assays (Life Technologies, Foster City, CA). miR-24-3p, miR-27a-3p, miR-142-5p, and miR-320b were negatively associated with the root mean of square of successive differences between adjacent normal NN intervals (RMSSD) (P(trend) = 0.006, 0.047, 0.019, 0.011, respectively). miR-142-5p and miR-320b were also negatively associated with standard deviation of all normal to normal NN intervals (SDNN) (P(trend) = 0.01 and 0.035). miR-24-3p, miR-27a-3p, and miR-320b were significantly interacted with multiple PAH metabolites and influenced heart rate variability indices, whereas miR-24-3p also significantly interacted with smoking to influence low frequency (P(interaction) < 0.05 for all). Plasma miRNAs might act as potential biomarkers for the adverse effect of PAH exposure on the cardiovascular system.