The invention relates to modified polyester and a preparation method thereof. Terephthalic acid, ethylene glycol and dihydric alcohol with branched chains are uniformly mixed and are then sequentiallysubjected to esterification reaction and condensation polymerization to obtain the modified polyester, wherein the dihydric alcohol with branched chains has the structural formula shown in the description; in the formula, R1 and R2 respectively and independently select straight chain alkylidene with the carbon number being 1 to 3; R3 selects alkyl with the carbon number being 1 to 5; R4 selects alkyl with the carbon number being 2 to 5. The molecular chain of the finally prepared modified polyester comprises a terephthalic acid chain segment, an ethylene glycol chain segment and a dihydric alcohol chain segment with branched chains; the content of annular low polymers in the modified polyester is smaller than or equal to 0.6 weight percent. The method has the advantages that the content of the annular low polymers in the modified polyester can be obviously reduced; the influence on the performance of the polyester pre se cannot be caused; the prepared modified polyester has high molecular weight; the distribution is narrow; good popularization values are realized.