[Objective] To investigate the differentially expressed proteins between isoniazid, streptomycin mono-and poly-drug resistant clinical isolate strains of Mycobacterium tuberculosis. [Methods] Cellular proteins were extracted from isoniazid, streptomycin mono-and poly-drug resistant clinical isolates M. tuberculosis and H37Rv. Differentially expressed proteins were identified through isobaric tags for relative and absolute quantification (iTRAQ) combined with Nano LC-MS/MS technology. The biological function and interaction among differentially expressed proteins and isoniazid or streptomycin were analyzed by DAVID 6.7 and STITCH 5.0, respectively. [Results] 58 differentially expressed proteins were identified in isoniazid, streptomycin mono-drug resistant strains and isoniazid, streptomycin poly-drug resistance strain compared with the proteomic profiles of H37Rv. The biological function of differentially expressed proteins mainly relates to oxidoreductase and transferase activity. Compared with isoniazid and streptomycin poly-drug resistance strain, two proteins (Rv2986c and Rv1908c) were up-regulated over 1.25 folds and two proteins (Rv3133c and Rv0577) were down-regulated less than 0.7 fold in isoniazid, streptomycin mono-drug resistant strains. Bioinformatics predicted that the four proteins interact with isoniazid and streptomycin directly or indirectly. [Conclusion] The expressed level or the interactions together of Rv2986c, Rv1908c, Rv3133c and Rv0577 is likely to be related to isoniazid and streptomycin resistance in M. tuberculosis.