The invention relates to a bio-based degradable polyester fiber and a preparation method thereof. The preparation method includes: adopting bio-based diol and bio-based binary acid as the raw materials, adopting melt polycondensation, carrying out esterification reaction, segmented pre-polycondensation reaction and final polycondensation reaction successively to obtain bio-based degradable polyester, and then conducting melt spinning forming to obtain the bio-based degradable polyester fiber. Specifically, the segmented pre-polycondensation reaction falls into first pre-polycondensation reaction and second pre-polycondensation reaction, wherein polyethylene glycol is added in the first pre-polycondensation reaction process, and a monomer with a polyhydroxyl structure is added in the secondpre-polycondensation reaction process. The final product has a moisture regain of greater than or equal to 2.0% and a surface contact angle of less than or equal to 60 degrees. The preparation methodprovided by the invention has a simple process, effectively reduces the duration of polycondensation reaction, lowers energy consumption and material consumption, and has good economic benefits. Theproduct prepared by the method provided b the invention has the advantages of good degradability, good fiber mechanical strength and high quality, and has great application prospects.