Many studies have investigated the effect of bisphenol A (BPA) exposure on gut microbial community changes, while the influence of gut microbiota on metabolism of BPA in organisms remains not well known. To explore this, in this study, Sprague-Dawley rats were intermittently (a 7-day interval) or continuously dosed by oral gavage at 500 µg BPA/kg bw/day for 28 days. Under a 7-day interval BPA exposure, the metabolism of BPA in rats and gut microbiota structure did not change greatly with dosing time. In contrast, following continuous BPA exposure, the relative abundances of Firmicutes and Proteobacteria in rat gut were significantly increased, and the alpha diversity of rat gut bacteria was greatly reduced. Meanwhile, the mean proportion of BPA sulfate to total BPA in rat blood was gradually decreased from 30 (day 1) to 7.4% (day 28). After 28 days of continuous exposure, the mean proportion of BPA glucuronide to total BPA in rat urine elevated from 70 to 81%, and in rat feces the mean proportion of BPA gradually decreased from 83 to 65%. Under continuous BPA exposure, the abundances of 27, 25, and 24 gut microbial genera were significantly correlated with the proportion of BPA or its metabolites in rat blood, urine, and feces, respectively. Overall, this study first demonstrates that continuous BPA exposure disrupted the rat gut microbiota community, which in turn altered the metabolism of BPA in rats. This finding contributes to the better understanding of metabolism of BPA in humans.