A biochemical viscosity reducer for heavy oil and a preparation method thereof. The viscosity reducer includes: Brevibacillus borstelensis-fermented mixed lipopeptide solution: 30 to 60 parts; compound biological enzyme: 15 to 30 parts; plant-based nonionic surfactant: 10 to 20 parts; antibacterial agent: 1 to 5 parts; stabilizer: 1 to 5 parts; and alcohol solvent: 10 to 20 parts; where, the above components are measured by mass. The preparation method includes: step 1: adding 30 to 60 parts of a Brevibacillus borstelensis-fermented mixed lipopeptide solution, 15 to 30 parts of a compound biological enzyme, 10 to 20 parts of a plant-based nonionic surfactant, and 1 to 5 parts of a stabilizer to a reactor; and step 2: adding 1 to 5 parts of an antibacterial agent and an alcohol solvent to the reactor, and stirring a resulting mixture for 60 min to 120 min.