Cytochrome bcc complex is important for ATP synthesis and cellular activity, as a crucial step in the terminal reduction of oxygen in aerobic electron transport chains. The b subunit of cytochrome bcc complex (QcrB) has been reported as a promising anti-tuberculosis target, with many novel anti-tuberculosis scaffolds reported. However, the 3D structure of mycobacterium tuberculosis (M. tuberculosis) QcrB has not been released, making it hard to understand the interactions between QcrB and its inhibitors as well as to develop novel anti-tuberculosis scaffolds. Herein we built the optimal homology model of M. tuberculosis QcrB using the M. smegmatis QcrB structure as template, which was refined through all-atom molecular dynamics simulation. Then, the binding modes of known inhibitors were predicted through molecular docking method, along with molecular dynamics simulation and binding free energy calculation to verify the accuracy of docking results and stability of the protein-inhibitor complexes. The informative key residues within QcrB site enabled us to perform structure-based virtual library screening to obtain potential M. tuberculosis QcrB inhibitors, which were validated through molecular dynamics simulation and MM-GBSA calculation and analyzed through pharmacokinetic properties prediction. Our research would provide a deeper insight into the interactions between M. tuberculosis QcrB and its inhibitors, which boosts to develop novel therapy against tuberculosis.Communicated by Ramaswamy H. Sarma.