The article describes the development of a robust pharmacophore model and the investigation of structure activity relationship (SAR) analysis of 3-nitro-1H-1,2,4-triazole-based aliphatic and aromatic amines analogs reported for anti-trypanosomal activity using PHASE module of Schrodinger software. The present works also encompass molecular interaction study of 3-nitro-1H-1,2,4-triazole-based aliphatic and aromatic amines analogs on maestro 8.5 workstation. The instant 3D QSAR is on anti-protozoan parasites, viz T. b. rhodesiense and L. donovani. The Phase study module comprises the five points pharmacophore model for the protozoan parasites activity, e.g. L.donovani (ADHRR.172), T.b. rhodesiense (ADHRR.1452). The pharmacophore models for anti-protozoan activities shares the common features, viz.consisting of one hydrogen bond acceptor (A), one hydrogen bond donor (D), one Hydrophobic (H) and two aromatic ring (R) and with discrete geometries as pharmacophoric feature. The developed pharmacophore model was used to derive a predictive atom-based 3D QSAR model. The obtained 3D QSAR model has an excellent correlation coefficient value (r2 ˂ 0.99) along with good statistical significance as shown by high Fisher ratio. The model also exhibits good predictive power, which is confirmed by high value of cross validated correlation coefficient (q2 ˂0.6). The QSAR model suggests that hydrophobic and aromatic characters are crucial for the anti-trypanosomal activity. The QSAR model also suggests that the inclusion of hydrophobic substituents would enhance the anti-trypanosomal activity. In addition to the hydrogen bond acceptor, hydrophobic character, positively contributes to the anti-trypanosomal activity. This study provides a set of guidelines for designing compounds with better anti-trypanosomal activity .