Considering atomic property vector and atomic correlative function, the 3-dimensional structural vector of atomic property correlation (3D-VAPC), a novel descriptor,is defined to characterize a 3-dimensional molecular structure by introducing self-adaptability regulation mechanism and the idea of orientating to customers. Characterizing the structures of 25 bisphenol A compounds by this vector, the QSAR models of three kinds of estrogen activities (ER affinities, gene induction and cell proliferation) have high multiple correlation coefficient (Rcum2=0.933, 0.813, 0.959) and cross verification coefficient (Qcum2=0.847, 0.953, 0.798) by support vector machine (SVM), which suits for nonlinear circumstances. The above results show that the models successfully express the correlation between structure and three kinds of estrogen activities. Therefore, 3D-VAPC exactly reflects the molecular structural information and SVM method correctly describes the correlation between information and property of the compounds.