The invention relates to a synthesis method of 5-oxa-nonanedioic acid, and mainly solves the technical problem of lack of effective synthesis methods of 5-oxa-nonanedioic acid. The synthesis method provided by the invention comprises the following steps: under protection of nitrogen, adding 4-bromobutyl benzyl ether into a dimethylsulfoxide (DMSO) solution of 1,4-butanediol and potassium hydroxideto generate a compound 1; carrying out catalytic debenzylation on the compound 1 by Pd/C in methanol in a hydrogen environment to generate a compound 2; and oxidizing the compound 2 by a Jones reagent in acetone to produce a target compound 3. The reaction formula is as follows. The synthesis method has the advantages of short reaction time, mild reaction, high product purity and high yield.