The invention discloses a method for preparing a zeolite socony mobil (ZSM)-5 zeolite secondary structural unit-containing molecular sieve. The method comprises the following steps of: treating ZSM-5 zeolite by using 0.5 to 3.0mol/L NaOH solution at the temperature of between 70 and 100 DEG C for 1 to 5 hours, wherein a liquid-solid ratio of the NaOH solution to the ZSM-5 molecular sieve is (10-30)ml:1g, rapidly cooling to room temperature, and performing filtration or high speed centrifugation to obtain zeolite precursor-containing nanocluster solution; and mixing the nanocluster solution and aqueous solution of hexadecyl trimethyl ammonium bromide, adjusting a pH value to 9.0 to 12.0 by using sulfuric acid, crystallizing at the temperature of between 90 and 120 DEG C for 12 to 72 hours,performing suction filtration, washing, drying, and roasting in air atmosphere at the temperature of 550 DEG C for 5 to 8 hours. The method has the characteristics of high hydrothermal stability and high and adjustable acidity, the crystallization process of forming zeolite nanoclusters is saved, the method is easy to operate, and the cost is reduced.