The invention relates to a preparation method of a ZSM-5 molecular sieve with a multi-level pore channel structure. The preparation method comprises the following steps of: performing activating treatment on natural layered clay by virtue of a high-temperature roasting mode; adding the activated natural layered clay into an acidic solution and performing acid treatment to obtain a mixture; adding water glass, a template agent and water sequentially into the mixture, so that the constitution of the mixture accords with the condition that the molar ratio of Na2O:Al2O3:SiO2:H2O is equal to (3-11):1:(20-100):(500-1500); adjusting the pH value of the mixture to 9-12 to obtain reactant gel; performing ageing treatment on the reactant gel; performing hydrothermal crystallization treatment on the aged reactant gel to obtain the ZSM-5 molecular sieve with the multi-level pore channel structure. By utilizing the method, the ZSM-5 molecular sieve with the multi-level pore channel structure is synthesized by taking the natural layered clay which is roasted at a high temperature as a unique aluminum source, taking the water glass as a supplemented silicon source and adopting the single template agent. The method has the advantages of simplicity and low cost.