The invention discloses a 1,4; 3, 6-diglycidyl hexanehexol modified PET polyester and a semi-continuous preparation method thereof, and monomers of the modified PET polyester comprise (a) terephthalic acid, (b) ethylene glycol, and (c) 1, 4; 3, 6-dihexanediol or mixtures thereof, and (d) aliphatic and / or alicyclic dihydric alcohol. The method comprises the following steps: preparing a certain amount of terephthalic acid glycol ester in a first esterification kettle, then continuously adding mixed terephthalic acid and glycol slurry into the first esterification kettle at a certain flow rate for reaction, and intermittently discharging reaction products into a second esterification kettle, and adding the modified monomer / ester exchange catalyst into the second esterification kettle for esterification / ester exchange reaction to obtain a prepolymer, discharging all the prepolymer into a polycondensation kettle, adding a polycondensation catalyst, and carrying out melt polycondensation to obtain a final polymer. The method provided by the invention overcomes the problems of low reaction activity, low conversion rate and high production cost of bio-based monomers, avoids the problem of metal residues, and is beneficial to realization of industrial production.