The invention belongs to the technical field of polymer synthesis, and particularly relates to a method for controlling the viscosity of a molybdenum-based catalytic butadiene polymerization system. The preparation method comprises the following steps: under the protection of nitrogen, adding a structure modifier into a mixture of butadiene and solvent oil, and carrying out a coordination polymerization reaction on the butadiene at 30-90 DEG C by adopting a molybdenum-based catalytic system to synthesize a polymer glue solution with Mooney viscosity and dynamic viscosity of 1-10*10<4> mPa.s, wherein the molybdenum-based catalytic system is composed of a main catalyst molybdenum compound, a cocatalyst aluminum alkyl compound and a ligand. According to the invention, the number-average molecular weight of the high polymer obtained by polymerization is 10<4>-10<5>, the viscosity of the glue solution is 1-10*10<4> mPa.S, the Mooney viscosity ML1+4<100> is 40 to 60, the content of the 1,2 structures is greater than or equal to 75%, the gel content is not higher than 1% of the butadiene polymerization product, the molecular weight distribution is wide, the viscosity is controllable, theconveying performance is good, and the product can be used for tire materials.