The invention discloses a preparation method of a polyester filler material containing isosorbide and methyl beta cyclodextrin. According to the method, a diacid part, methyl beta cyclodextrin and anisosorbide part are taken as monomers, stannous pyrophosphate is taken as a catalyst for reaction, and polyester is prepared by utilizing existing polymerization equipment at enough temperature and pressure. The stannous pyrophosphate is a non-toxic organic metal catalyst, and when the polymer is applied to medicines, human bodies, agriculture and the like, the property is very important. According to the method, the temperature required by reaction can be reduced, the loss of raw materials in the system is reduced, the occurrence probability of side reaction is reduced, and the molecular weight is not reduced. Meanwhile, when stannous pyrophosphate is left in the polymer, the settling velocity of the coating filler can be reduced, and the filler performance is improved. Meanwhile, the methyl beta ring paste is used as an embedded part to be inserted into a polyester polymer structure, the material mobile phase selection range is wide, high pressure resistance is achieved, and the method can be applied to microsphere filler or coating filler.