The invention relates to a synthesis method of 2-amino-5-pyrimidine pinacol borate. The preparation method is characterized by comprising the following steps of: reacting 2-amino-5-bromo pyrimidine with ditertbutyl dicarbonate under the catalysis action of 4-dimethylaminopyridine to obtain a product in which an amino group at the second position in pyrimidine is protected by two tertiarybutoxy carbonyl groups; carrying out lithiation on the obtained product under the action of nbutyl lithium, reacting with the lithiated product with triisopropyl borate under the protection of nitrogen at a temperature between 70 DEG C below zero and 80 DEG C below zero so that bromine at the fifth position is converted into boric acid, wherein a tertiarybutoxy carbonyl group possibly falls off from a part of the product on a quenching condition so as to finally obtain a product which is a compound; removing the tertiarybutoxy carbonyl group serving as a protection group from the obtained product under the action of acid so as to obtain 2-amino pyrimidine-5-boric acid; carrying out reflux and water distillation on the obtained 2-amino pyrimidine-5-boric acid and pinacol in an organic solvent to obtain 2-amino-5-pyrimidine pinacol borate. The preparation method has the advantages of simple process and high production efficiency and can be applied to mass production.