Quantitative structure activity relationship (QSAR) has been established between the various physiochemical parameters of a series of nitazoxanide-based analogues and its antibacterial activity against Clostridium difficile. Genetic function approximation (GFA) and comparative molecular field analysis (CoMFA) techniques were used to identify the descriptors that have influence on biological activity. The most influencing molecular descriptors identified in 2D-QSAR include spatial, topological, and electronic descriptors, while electrostatic and stereoscopic fields were the most influencing molecular descriptors identified in 3D-QSAR. Statistical qualities (r2, q2) indicated the significance and predictability of the developed models. The study indicated that antibacterial activity of Clostridium difficile can be improved by increasing molecular connectivity index, local charge surface index, sharp index and decreasing molecular flexibility index.