Abstract: The nuclear magnetic resonance (NMR) spectroscopy technology is one of the important methods in chemical structure identification. In this paper, the basic principle of NMR was introduced, and the applications of NMR for identifying the structures of antibiotic peptides and lipopeptides of Bacillus subtilis were summarized. Finally, the progress of NMR combined with other techniques was stated and the application of these combined techniques in identification of new antimicrobial compounds from Bacillus subtilis was prospected.