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 alkaline protease was applied for CSM property improvement, including free gossypol removal, protein solubility, and bioactive compounds content in the present study. A maximal extent of 78% for free gossypol removal and an increase of total soluble protein content to 58.11% were 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 analysis 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 was involved in the metabolisms of carboxylic acids, benzene, glycerophospholipid, allyl alcohol lipids, steroids, flavonoids, phenols, and their derivatives. The fermented CSM also showed improved angiotensin I-converting enzyme inhibition (86.72%) and antioxidant activities (87.51%) which might be due to the bioactive compounds generated by the cooperation of B. subtilis and kefir flora.