The invention discloses a clean metallurgic method for preparing ammonium molybdate from molybdenite concentrates. The traditional limestone roasting and ammonium carbonate solution leaching method is abandoned to ensure that an ammonium sulfate solution in a mother solution does not form a low-value ammonium sulfate byproduct to be discharged from a production system again, but is efficiently converted into an ammonium carbonate solution through adding cheap and available calcium carbonate, so that the circulation of ammonium/ammonia in the system is realized, and furthermore all the solutions in the system can be recycled; in addition, an intermediate product is ammonium polymolybdate obtained through acid precipitation so as to facilitate carrying out a preparation process for a subsequent molybdenum product. The clean metallurgic method concretely comprises the steps of raw material configuration; oxidizing roasting; pretreatment; ammonium salt leaching; purification and separation; acid precipitation and separation; ammonium salt conversion and separation; and recovery and absorption, wherein an ammonium salt solution leaching agent required in the leaching step is prepared by adding the NH3 and CO2 gases obtained in the production process and the ammonium carbonate solution obtained after absorption and replenishing a proper quantity of ammonia water. The clean metallurgic method is low in production cost and high in production efficiency.