The invention discloses a composite bacillus cottonseed meal fermenting agent and a preparation method thereof. The preparation method comprises the following steps of: performing expanding culture on strains of bacillus subtilis, bacillus natto, brevibacillus laterosporus and bacillus coagulans by a liquid fermentation method; inoculating into a fermentation tank to ferment; adding a carrier to adsorb; drying at low temperature; and mixing in a ratio to prepare the composite bacillus cottonseed meal fermenting agent, the total microbial content of the fermenting agent is more than or equal to 100*108 CFU/G. The composite bacillus cottonseed meal fermenting agent can effectively inhibit growth of miscellaneous bacteria in the fermentation process of the cottonseed meal, reduce the free gossypol content of the cottonseed meal and increase the protein content and the free amino acid content of the cottonseed meal, and has the characteristics of simple preparation process, stable and reliable production quality, low cost and the like.