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Bisphenol A (BPA) is a ubiquitous environmental pollutant with endocrine-disrupting functions. Identifying protective drugs and exploring the mechanisms against BPA are crucial in healthcare. Natural products exhibiting antioxidant properties are considered to be able to protect against BPA toxicity. Although BPA-modulated targets and miRNAs have been individually reported, their connections to natural products were rarely organized. With the help of a protein–protein interaction database (STRING), the relationship between individual BPA-modulated targets was interconnected to provide a systemic view. In this review, BPA-downregulated and -upregulated targets are classified, and their interactive network was innovatively analyzed using the bioinformatic database (STRING). BPA-modulated miRNAs were also retrieved and ingeniously connected to BPA-modulated targets. Moreover, a novel connection between BPA-countering natural products was integrated into BPA-modulated miRNAs and targets. All these targets-associated natural products and/or miRNAs were incorporated into the STRING network, providing systemic relationships. Overall, the BPA-modulated target–miRNA-protecting natural product axis was innovatively constructed, providing a straightforward direction for exploring the integrated BPA-countering effects and mechanisms of natural products.