The invention relates to a farmland heavy metal contaminated soil compound modifying agent and a preparation method and an application method thereof. The farmland heavy metal contaminated soil compound modifying agent comprises, by weight, 20-40% of activated decomposed coal, 15-25% of charcoal, 10-25% of sepiolite, 10-20% of calcium magnesium phosphate fertilizer and 10-20% of diammonium phosphate, wherein the activated decomposed coal is obtained by activating ammonium bicarbonate and ultrasonic waves, and the sepiolite is obtained by pyrolysis at the temperature of 600-800 DEG C. The farmland heavy metal contaminated soil compound modifying agent is low in cost and simple in formula and mainly used for passivating heavy metal of Cd, Cu, Pb and Zn in soil, the soil polluted by the heavy metal can be effectively repaired, the sustainable production capacity of the soil can be ensured, and the sustainable soil utilization is achieved.