The invention belongs to the field of wet smelting, and particularly relates to a treatment method of tertiary ammonia leaching residues in the ammonium molybdate production process. The method comprises the steps that the tertiary residues are subjected to the processes of acid treatment, ammonia leaching, impurity removing and neutralization and crystallization, wherein the impurity removing process comprises the step that ammonia liquor is treated by adopting a series of reagents such as ammonium carbonate, ammonium sulfide, hydrogen peroxide and magnesium nitrate according to a specific proportion to decrease or eliminate the content of impurities in ammonia leaching liquor. The method has the advantages that by adopting the technical scheme, the processes are simple, the treatment efficiency is improved, ammonium molybdate prepared through the method is good in quality, and the production cost is reduced; the product is low in impurity content and white in color and luster and meets the national standard.