Objective To investigate the anti-estrogenic activity of bisphenol A and its substitutes, and to analyze the relevant mechanisms. Methods Bisphenol A and its three most widely used substitutes (bisphenol S, bisphenol F and bisphenol AF) were selected as the docking ligand molecules, and estradiol was used as the control ligand molecule. The ligand molecules docking was simulated with estrogen receptor (ER) α and ERβ using AutoDock software. Results Bisphenol A forms a hydrogen bond with ERα at the His474 residue and with ERβ via three hydrogen bonds at Leu260, His428, and Asn431 residues. Similar to bisphenol A, bisphenol S, bisphenol F, bisphenol AF and estradiol primarily interact with ERα and ERβ through hydrophobic interactions and hydrogen bonds, but with varying optimal binding sites and affinities. The binding forces of the optimal binding sites for bisphenol A, bisphenol F, bisphenol AF, bisphenol S and estradiol with ERα were -4.15, -4.19, -2.73, -4.62 and -5.37 kcal/mol, respectively, and with ERβ were -3.76, -3.91, -2.86, -3.93, and -4.98 kcal/mol, respectively. The affinity ranking for two ERs with these five molecules from high to low was estradiol > bisphenol S> bisphenol F> bisphenol A > bisphenol AF. Conclusion The affinity between bisphenol compounds with ERα and ERβ is mainly based on the hydrophobic interaction with non-polar residues of the receptor and hydrogen bonding with key residues. Bisphenol S, bisphenol F and bisphenol AF showed similar or even stronger endocrine disrupting effects than bisphenol A.