Cottonseed meal (CSM), a high-protein-content waste from the cottonseed oil industry, shows potential application as an animal feeding resource, which is hindered by its endogenous antinutritional factor (free gossypol).Microbial fermentation of CSM by the synergistic action of Bacillus subtilis, kefir flora and alk. protease was applied for CSM property improvement, including free gossypol removal, protein solubility and bioactive compounds content in present study.A maximal extent of 78% for free gossypol removal and an increase of total soluble protein content to 58.11% achieved under the optimal fermentation conditions obtained via BBD-RSM design.The volatile base nitrogen reduction and bioactive peptides synthesis were also observed in the fermented CSM.The anal. results of metabolomics and metagenomics by integrated metabolomics and metagenomics techniques indicated the microorganism consortium secreted multiple enzymes for proteolysis and resulted in the variation of metabolite composition which involved in the metabolisms of carboxylic acids, benzene, glycerophospholipid, allyl alc. lipids, steroids, flavonoids, phenols, and their derivativesThe fermented CSM also showed improved angiotensin I-converting enzyme inhibition (86.72%) and antioxidant activities (87.51%) with might due to the bioactive compounds generated by the cooperation of B. subtilis and kefir flora.