[Objective] To establish a high-throughput drug screening model for screening inhibitors of Mycobacterium tuberculosis Phenylalanyl-tRNA synthetase (PheRS). [Methods] In this work, Mycobacterium tuberculosis pheRS gene was cloned and overexpressed in E. coli, and then the purified recombinant enzyme was used to establish an high-throughput drug screening model. After establishment and optimization of the screening assay, a primary screening was performed with compounds library and microbial fermentation collection in our institute, and their anti-bacterial activity and cytotoxicity were assessed further. [Results] 9 out of 11 600 compouds and 37 out of 5 200 microbial fermentation samples were identified as primary hits. [Conclusion] 6 microbial fermentation samples inhibited enzymatic activity of PheRS in vitro and growth of Mycobacterium smegmatis, and showed lower cytotoxicity.