The invention relates to a novel process for preparing azelaic acid monomethyl ester based on biodiesel. The novel process is characterized in that the biodiesel is used as a raw material, a C18 methyl ester cracking raw material with an unsaturated fatty acid methyl ester content greater than 99.8% is separated and obtained through high vacuum distillation and freezing crystallization, and then azelaic acid monomethyl ester, malonic acid, caproic acid, and nonanoic acid are obtained through ozone oxidative cleavage reaction, separation and purification. The process has the characteristics ofsimple process, environment-friendly oxidation mode, non-pollution, and high added value of the product; and the beneficial effects are that a large amount of high-purity azelaic acid monomethyl estercan be obtained, the mass fraction of the azelaic acid monomethyl ester is higher than 99%, and by-products of malonic acid, caproic acid and nonanoic acid are obtained, thereby improving the added value of the biodiesel, and promoting rapid development of biodiesel industry.