The invention relates to a biological enzyme preparation fertilizer formula and a processing method thereof, wherein the enzyme preparation fertilizer is one stage higher than biological bacterium fertilizer. The biological enzyme preparation fertilizer formula comprises the steps of evenly mixing excrements of livestocks, rice hull powder, fermenting enzyme preparation, mineral powder and the like, performing fermentation, screening and drying stone sundries after temperature reaches 60-65 DEGC and harmful bacteria are almost completely killed,, then adding nutrient elements and enzymic preparations with different contents according to requirements of soil and plants; evenly stirring, then utilizing a drying method pelletizer to prilling, and directly bagging. After being fertilized to soil, the fertilizer can efficiently increase production, improve soil, recover soil fertility, improve fertilizer efficiency, decompose heavy metals in soil, improve ground temperature and water temperature, and promote prematurity. Beneficial bacteria are bred, and harmful bacteria are perished. Plants are enabled to be robust, root systems are enabled to be developed, stress resistance of plants is increased, plant live stems are enabled to mature, thousand seed weight of rice is increased, hundred-grain weights of corn and soybean are increased, and pesticides are applied less or not applied. Milled rice rate of rice is high, commodity rate of vegetables and melons is high, chemical fertilizer and pesticide pollution is greatly reduced, the ecological agriculture target is achieved, and large-scale agriculture is led to the road of virtuous circle.