Mycobacterium tuberculosis (MTB) PknG, one of 11 Ser/Thr protein kinases produced by MTB, plays an essential role in the residing of MTB in the macrophages as persistent state. In this work, we amplified the pknG gene from the genome of H37Rv, and constructed a recombinant plasmid pET-pknG to express the PknG protein in the E. coli. Using purified PknG, we established and optimized a high-throughout screening model to screen for PknG inhibitors. Among 2120 samples of microbial fermentations and 2300 samples of compounds tested, one positive compound and 13 positive fermentation samples were identified with inhibitory effect on activity of PKnG, resulting in a 0.32% of positive rate.