Inducible nitric oxide synthase(iNOS), which can produce nitric oxide(NO) in the induction of cytokines and other factors, has an important impact onthe physiological functions of the body for the transmission of information. However,continuous generation of NOwill produce a lot of great damages to organisms. Therefore, iNOS inhibitors with good inhibitory activity and selectivity have beenimportant means of treating a variety of diseases. Based on the public-alignment of pteridine, 3D-QSAR(Three-Dimensional Quantitative Structure-Activity Relationship) models of pteridine analogues as iNOS inhibitors were established by the 3D-QSAR protocol of Discovery Studio 3.0. Pteridine molecules divided in different groups obtained four approximate models, indicating good stability of such models, in which A3 is preferable(q2= 0.672, r2= 0.996, rpred2. = 0.888, q2denotes the cross-validation coefficient, r2denotes the non-cross-validation coefficient). This study should be significant for the future structure design and modification of pteridine analogues as iNOS inhibitors.