The invention discloses a biological enzyme cleaning agent and a method for preparing the biological enzyme cleaning agent. The biological enzyme cleaning agent comprises a solution A and a solution B; the solution A comprises the following components in parts by weight: 70-90 parts of protease solution, 0.2-1.0 part of borax, 0.5-2.0 parts of sodium citrate, 5-10 parts of glycerin and 5-10 partsof anhydrous ethanol; and the solution B comprises the following in parts by weight: 10-20 parts of sodium dodecyl benzene sulfonate, 15-30 parts of alkylphenol polyoxyethylene, 10-15 parts of fatty alcohol polyoxyethylene ether, 5-10 parts of glycerol, 0.5-1.0 part of borax, 1-2 parts of sodium citrate, 10-20 parts of anhydrous ethanol, 0.5-1.0 part of lipase, 0.5-1.5 part of amylase, 0.5-1.5 part of cellulose and 0.5-1.5 parts of lysozyme; the solution A and the solution B are stored separately; and when in use, the solution A and the solution B are mixed uniformly according to the weight ratio of 1:6 to 1:9. The biological enzymes in the biological enzyme cleaning agent have high activity, and the biological enzyme cleaning agent has a good cleaning effect and a strong sterilizing capacity.