The invention discloses a preparation method of 7-amino-3-methoxymethyl-3-cephem-4-carboxylic acid, and relates to the technical field of preparation of pharmaceutical intermediates. The method includes the steps that under the protection of nitrogen, 7-aminocephalosporanic acid, a silane reagent and an imidazole catalyst are stirred for 0.5-2 h at 30-35 DEG C in a water-soluble organic solvent; then, the mixture is cooled to 0-5 DEG C, methanesulfonic acid, trimethyl borate and methyl alcohol are added, a methoxylation reaction is conducted with the temperature controlled to be 0-5 DEG C, and 7-amino-3-methoxymethyl-3-cephem-4-carboxylic acid is obtained, wherein the silane reagent is hexamethyldisilazane or trimethylchlorosilane or N,O-bis(trimethylsilyl)acetamide or dimethoxydimethylsilane. According to the method, the product purity is high, the impurity content is low, operation is easy and convenient, refining steps are simplified, production cost is reduced, and the method is suitable for industrial production.