As a tumor suppressor, p53 protein regulates the cell cycle and is involved in preventing tumorgenesis. The protein level of p53 is under the tight control of its negative regulator human double minute 2 (HDM(2)) via ubiquitination. Therefore, the design of inhibitors of HDM(2) has attracted much interest of research on developing novel anticancer drugs. Presently, two classes of molecules, i.e., the 1,4-benzodiazepine-2,5-diones (BDPs) and N-Acylpolyamine (NAPA) derivatives were studied by three-dimensional quantitative structure-activity relationship (3D-QSAR) modeling approaches including the comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) as promising p53-HDM(2) inhibitors. Based on both the ligand-based and receptor-guided (docking) alignments, two optimal 3D-QSAR models were obtained with good predictive power of q(2) = 0.41, r(2)(pred) = 0.60 for BDPs, and q(2) = 0.414, r(2)(pred) = 0.69 for NAPA analogs, respectively. By analysis of the model and its related contour maps, it is revealed that the electrostatic interactions contributed much larger to the compound binding affinity than the steric effects. And the contour maps intuitively suggested where to modify the molecular structures in order to improve the binding affinity. In addition, molecular dynamics simulation (MD) study was also carried out on the dataset with purpose of exploring the detailed binding modes of ligand in the HDM(2) binding pocket. Based on the CoMFA contour maps and MD-based docking analyses, some key structural aspects responsible for inhibitory activity of these two classes of compounds were concluded as follows: For BDPs, the R(1) and R(3) regions should have small electronegativity groups; substituents R(2) and R(4) should be larger, and R(3) substituent mainly involves in H-bonds forming. For NAPA derivatives, bulky and electropositive groups in ring B and ring A, small substituent at region P is favorable for the inhibitory activity. The models and related information, we hope, may provide important insight into the inhibitor-p53-HDM(2) interactions and be helpful for facilitating the design of novel potent inhibitors.