The invention discloses a ZSM-48 molecular sieve with a low silica-alumina ratio and a preparation method thereof. The molecular sieve has the following properties: the molar ratio of silica to alumina is 25-50; the specific surface is 250-400 m2/g; the pore volume is 0.25-0.35 cm3/g; the average pore size is 3-5 nm. The preparation method comprises the following steps: (1) well mixing a seed crystal S, a template R, a silicon source, an aluminium source, sodium hydroxide and water to prepare a reaction mixture, wherein the composition of the reaction mixture is as follows: on a basis of oxide, the molar ratio of R to SiO2 is 0.05-0.2, the molar ratio of SiO2 to Al2O3 is 30-50, the molar ratio of Na2O to SiO2 is 0.06-0.1, the molar ratio of H2O to SiO2 is 15-23, the mass ratio of S to SiO2 is 0.05-0.5, S is the ZSM-48 molecular sieve, and R is 12-crown ether-4; (2) performing hydrothermal crystallization of the reaction mixture prepared in step (1) at 150-170 DEG C for 4-8 days, performing filtration, washing, drying, and roasting of the crystallization product to obtain the ZSM-48 molecular sieve with a low silica-alumina ratio. The ZSM-48 molecular sieve prepared by the method of the invention has a low silica-alumina ratio, and has good application prospects in technical fields of isodewaxing and the like.