Bisphenol A (BPA) is an endocrine disruptor with potentially harmful effects on humans. However, epigenetic mechanisms that modulate the effects of BPA remain unclear. Methylation of long interspersed nucleotide elements (LINE-1) is a marker of genome-wide methylation status. This study aims to examine whether BPA exposure was associated with LINE-1 methylation changes in men. Male factory workers in Hunan, China (N = 149) were studied, 77 with BPA exposure in workplace (BPA-exposed group) and 72 without BPA exposure in workplace (control group). Pre-shift and post-shift urine samples were collected from the BPA-exposed group and spot urine samples were collected from the control group. Urine samples were assessed for BPA. In addition, blood and semen samples were collected from both groups for LINE-1 methylation analysis. In multivariate analysis adjusted for age, education, smoking habits and alcohol consumption, sperm LINE-1 methylation level was significantly lower in BPA exposed workers (p < 0.001) compared to that in the unexposed workers. Linear regression analysis also showed that log-transformed urine BPA levels were inversely associated with sperm LINE-1 methylation (p < 0.0001), but not peripheral blood cell LINE-1 methylation. Moreover, the association between urine BPA level and semen quality was not attenuated after adjustments for LINE-1 level. In summary, the observed independent relationship between BPA exposure and LINE-1 methylation may have public health implications on reproductive health in men because of ubiquitous exposure to BPA.