The invention relates to a polyphosphoric acid ammonium selenide compound fertilizer and a preparation method thereof. The chemical composition expression of the polyphosphoric acid ammonium selenide compound fertilizer is (NH4)2nSen/2(PO3)3n, wherein n is a positive integer which is not smaller than 1. The preparation method for the polyphosphoric acid ammonium selenide compound fertilizer comprises the following steps: carrying out concentration on phosphoric acid to obtain polyphosphoric acid; carrying out fusion blending on ammonium nitrate, ammonium phosphate and urea to obtain fusion mixture; adding selenium powder and polyphosphoric acid into the fusion mixture, and reacting at the temperature of 130-170 DEG C at reaction time of 20-60min to obtain the polyphosphoric acid ammonium selenide compound fertilizer. The polyphosphoric acid ammonium selenide compound fertilizer is favorable for crops to adsorb selenium elements, and the utilization ratio of selenium can be effectively improved. The preparation method is simple in operation and is easy in realizing industrialization.