Over the years development of selective estrogen receptor (ER) ligands has been of great concern to researchers involved in the chemistry and pharmacology of anticancer drugs, resulting in numerous synthesized selective ER subtype inhibitors. In this work, a data set of 82 ER ligands with ER alpha and ER beta inhibitory activities was built, and quantitative structure-activity relationship (QSAR) methods based on the two linear (multiple linear regression, MLR, partial least squares regression, PLSR) and a nonlinear statistical method (Bayesian regularized neural network, BRNN) were applied to investigate the potential relationship of molecular structural features related to the activity and selectivity of these ligands. For ER alpha and ER beta, the performances of the MLR and PLSR models are superior to the BRNN model, giving more reasonable statistical properties (ER alpha: for MLR, R-tr(2) = 0.72, Q(te)(2) = 0.63; for PLSR, R-tr(2) = 0.92, Q(te)(2) = 0.84. ER beta: for MLR, R-tr(2) = 0.75, Q(te)(2) = 0.75; for PLSR, R-tr(2) = 0.98, Q(te)(2) = 0.80). The MLR method is also more powerful than other two methods for generating the subtype selectivity models, resulting in R-tr(2) = 0.74 and Q(te)(2) = 0.80. In addition, the molecular docking method was also used to explore the possible binding modes of the ligands and a relationship between the 3D-binding modes and the 2D-molecular structural features of ligands was further explored. The results show that the binding affinity strength for both ER alpha and ER beta is more correlated with the atom fragment type, polarity, electronegativites and hydrophobicity. The substitutent in position 8 of the naphthalene or the quinoline plane and the space orientation of these two planes contribute the most to the subtype selectivity on the basis of similar hydrogen bond interactions between binding ligands and both ER subtypes. The QSAR models built together with the docking procedure should be of great advantage for screening and designing ER ligands with improved affinity and subtype selectivity property.