The global pandemic of multidrug-resistant (MDR) Mycobacterium tuberculosis (TB) drives for more effective anti-TB drugs with new drug target. Filamentous temperature sensitive protein Z (FtsZ), a GTP dependent prokaryotic cell division protein, forms a dynamic Z-ring in the center of the cell. Differences between bacterial FtsZ and eukaryotic tubulin make FtsZ a highly attractive drug target. In this study, we used phenotype screening of M. smegmatis and model screening targeting M. tuberculosis FtsZ (Mtb-FtsZ) to identify a hit compound TB-E12. TB-E12 was found to prevent the growth of M. smegmatis by inhibiting the GTPase activity of Mtb-FtsZ. Molecular docking and site-directed mutagenesis analyses identified Asn22 of Mtb-FtsZ as the key amino site. The higher MIC of TB-E12 for M. smegmatis strain overexpressing Mtb-FtsZ confirmed that Mtb-FtsZ is likely the target. Importantly, TB-E12 exhibits excellent anti-TB activity, but had no anti-bacterial activity to other strains. In vitro, the proliferation of Mycobacterium smegmatis was inhibited by TB-E12. All these results indicate TB-E12 is a promising lead compound against drug-resistant tuberculosis.