Estrogen receptors (ERs) are significant protein targets that can alter normal homeostatic transcription and signaling pathways. And the development of selective ER ligands is involved in the pharmacology of anticancer drugs, leading to the synthesis of numerous ER selective ligands. In the present work, three dimensional quantitative structure–activity relationship (3D-QSAR) models, including comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) in combination with molecular docking were performed on a series of ER ligands to investigate the potential relationship between the structural features of the compounds and its activity and selectivity. Good statistical significance was achieved for the CoMFA (ERα: R2cv = 0.676, R2pred = 0.631. ERβ: R2cv = 0.578, R2pred = 0.5341) and CoMISA (ERα: R2cv = 0.693, R2pred = 0.5758. ERβ: R2cv = 0.653, R2pred = 0.615) models. In addition, molecular docking results confirmed that the substituents at ring A, ring D and ring E were crucial for interacting with receptors ERα and ERβ, respectively, which were in agreement with the QSAR results. The substituents in ring A and ring F for ERα and residues Thr347/Ala302, Met388/Leu343, Leu391/Arg346, Met421/Ile376, Gly521/Leu476 for ERα and ERβ, respectively, contribute the most to the subtype selectivity. These results obtained from this work provide valuable information for the design of novel selective ER ligands with enhanced activity.