The invention provides a method for preparing an MCM-49 molecular sieve containing rare earth. The molecular sieve comprises the following raw materials: an aluminum source, a base source, a silicon source, hexamethylene imine, cyclohexane, deionized water and salts of the rare earth, wherein the molar ratios of the raw materials comprise: SiO2:Al2O3 is 12-50, OH:SiO2 is 0.05-0.7, (HMI+CHA):SiO2 is 0.08-1.2, H2O:SiO2 is 10-70, and Re2O3:Al2O3 is 0.01- 0.5. The method comprises the following steps: putting the raw materials into a synthesizing kettle according to the ratios, and sealing the kettle; raising programming temperature to a crystallization temperature of between 135 and 180 DEG C; and then crystallizing and cooling the raw materials in self-generated pressure; and obtaining the MCM-49 molecular sieve containing the rare earth after a crystallized product is subjected to filtering, washing and drying. The method can improve the stability of a molecular sieve catalyst by introducing the rare earth into the molecular sieve in synthesizing, and obviously reduce the synthesizing cost by replacing partial or most of the hexamethylene imine by the cyclohexane in organic amine; meanwhile, the preparation method has the characteristics of good repeatability and high degree of crystallinity of the product.