Bacillus subtilis strain Z15 (BS-Z15) was isolated from the cotton field of Xinjiang, China, and characterized as an effective biocontrol agent antagonizing plant pathogen Verticillium dahliae 991 (VD-991). However, the chemical substance produced by BS-Z15 for resistance to VD-991 remains elusive. Here, a serial purification methods including HCl precipitation, organic solvent extraction, and separation by semi-preparative High-Performance Liquid Chromatography were performed to obtain a single compound about 3.5 mg/L from the fermentation broth of BS-Z15, which has an antifungal activity against VD-991. Moreover, Fourier Transform Infrared spectrum, Nuclear Magnetic Resonance Spectroscopy, and Tandem Mass Spectrometry analyses were carried out to finally confirm that the active compound from BS-Z15 is a mycosubtilin homologue with C17 fatty acid chain. Genomic sequence prediction and PCR verification further showed that the BS-Z15 genome contains the whole mycosubtilin operon comprising four ORFs: fenF, mycA, mycB, and mycC, and the expression levels of mycA-N, mycB-Y and mycC-N reached a peak at 32-h fermentation. Although mycosubtilin homologue at 1 μg/mL promoted the germination of cotton seed, that with high concentration at 10 μg/mL had no significant effect on seed germination, plant height and dry weight. Furthermore, mycosubtilin homologue sprayed at 10 μg/mL on two-week-old cotton leaves promotes the expression of pathogen-associated genes and gossypol accumulation, and greatly decreases VD-991 infection in cotton with disease index statistics. This study provides an efficient purification strategy for mycosubtilin homologue from BS-Z15, which can potentially be used as a biocontrol agent for controlling verticillium wilt in cotton.