The invention discloses a biodegradable sulfo-aliphatic aromatic polyester and a preparation method thereof. The preparation method comprises that thiodipropionic acid and aromatic diol undergo an esterification reaction at 150-190 DEG C in the presence of a catalyst in a nitrogen gas protective atmosphere to produce an intermediate product, the introduction of nitrogen gas is stopped, the intermediate product undergoes a polycondensation reaction at 190-230 DEG C in a vacuum state to produce a polymer, an organic solvent is added into the polymer so that a clear solution is obtained after a large part of the polymer is dissolved, the clear solution is added into an alcohol solvent drop by drop so that white precipitates are produced, the precipitates are subjected to centrifugal separation so that white solids are obtained, and the white solids are subjected to alcohol washing and drying so that the biodegradable sulfo-aliphatic aromatic polyester is obtained. The preparation method can synthesizes the sulfo-aliphatic aromatic polyester material having good use performances and excellent degradation performances.