The cottonseed meal fermented by Bacillus was used in this study to investigate the effects on the degradation rate of free gossypol in cottonseed meal, as well as the effects on the nutrient components before and after fermentation, such as viable count bacteria, neutral proteases activity and acid-soluble protein content.. In addition, the strains with better fermentation effects were used for identification, and safety analysis and fermentation techonlogy were also performed. The results showed that the Bacillus subtilis, which could efficiently degrade the free gossypol and improve the nutritional quality of cottonseed meal, was BLCC1-0039, and the free gossypol was determined by high performance liquid chromatography. The BLCC1-0039 was preliminarily identified as the Bacillus subtilis by the morphology, and by the biochemical characteristics combined with 16S rDNA sequence. Thein vivo safety evaluation of B.BLCC1-0039 showed that no morphological and activity abnormalities appeared for the mice used, and no organ lesions were observed, which preliminarily suggested the safety of B.BLCC1-0039. Also, the fermentation induced by B.BLCC1-0039 could effectively reduce the content of free gossypol in cottonseed meal and improve the neutral proteases activity and acid-soluble protein content, the acid soluble protein was 26.96%, the activity of neutral protease was 3897 U/g and the degradation rate of free gossypol was 97.81% after fermentation for 48 h.