Hepatitis C virus (HCV) infects approximately 325 million individuals globally causing hepatitis C, a fatal disease leading to liver cirrhosis. Imperative sincere efforts are needed to develop inhibitors targeting the essential NS3/4A protease. NS3/4A protease is an exceptionally significant target. Resistance against the most promising protease inhibitors, Telaprevir, Boceprevir and Faldaprevir has emerged in clinical trials. The emergence of resistance is attributed to the error-prone viral RNA-dependent RNA polymerase, thereby reducing the effectiveness of these inhibitors. Among the drug-resistant variants, single amino acid residues (V35M, Q80K, R155K, A156V, and D168A) are noteworthy for their presence in clinical isolates and also their efficacy against these inhibitors in clinical development. Thus, it is essential to unravel the mechanistic insights of these drug-resistant variants while designing potent novel inhibitors. In this current work, we have performed molecular docking and comparative MD simulation to analyze and unravel molecular mechanism of conformational fluctuations among inhibitor binding between wild type and its V35M, Q80K, R155K, A156V, and D168A variants. Protein-ligand contacts, Root mean square deviation (RMSD), Root mean square fluctuation(RMSF) and post-simulation plot analysis has been used to identify the stability and conformation of the key residues that regulate inhibitor binding and their impact in developing drug resistance. Unraveling and understanding of the binding mechanism of inhibitor within substrate would be a significant approach to design inhibitor that fits within the substrate with less susceptibility towards drug resistance as mutations upsetting inhibitor binding would concurrently impede the recognition of viral substrates.