Arylamides have been identified as direct InhA inhibitors which overcome the drug-resistance problem of isoniazid, the first-line drug for tuberculosis treatment. However, arylamide properties are not yet optimal against Mycobacterium tuberculosis. Arylamides show high potency in InhA enzyme assay, but they fail in antimycobacterial assay. To achieve the structural basis to improve antimycobacterial activity, the dynamic behavior of arylamide inhibitors and a substrate, trans-2-hexadecenoyl-(N-acetylcysteamine)-thioester, were carried out by molecular dynamics (MD) simulations. Arylamide inhibitors and a substrate are positioned at the same site which indicates the competitive inhibitor function of arylamides. Based on our findings, the amide carbonyl oxygen causes the selectivity of arylamide inhibitors for InhA inhibition. Moreover, this moiety is crucial for the affinity of the arylamide-InhA interactions with Tyr158 and NADH to form hydrogen bonds. It is possible to enhance the selectivity of arylamide inhibitors to reach the InhA target by introducing a hydrophilic substituent into the aryl ring A. In order to increase the membrane permeability of arylamide inhibitors, more lipophilic properties should be incorporated into the substituent B. Therefore, based on the obtained results, the correct balance between the selectivity and the membrane permeability of arylamide inhibitors should improve their inhibitory activity against M. tuberculosis strain.