The invention discloses a medical stone fertilizer-medicine dual-effect multielement compound fertilizer and a preparation method thereof. The product is prepared by mixing medical stone, attapulgite, monoammonium phosphate (or diammonium phosphate), urea, ammonium chloride, potassium oxide, borax, aluminium potassium sulfate, agricultural Chinese herbs (cassava, liquorice, litsea cubeba, magnolia biloba, Chinese stellera root, red-knees herb, dragon juniper stems and leaves, common threewingnut root, yellow azalea, sun euphorbia herb and tobacco stem powder), a DA-6 plant growth regulator, a polyaspartic acid (PASP) plant nutrient promoter, an ethylene diamine tetraacetic acid (EDTA) ion chelant and the like. The product integrates fertilizers and medicines, contains all nutrient elements necessary for growth and ripeness of crops, has balanced fertilizer supply and long fertilizer efficiency, and can activate and utilize residual fertilizer in soil, immobilize and utilize a nitrogen element in air, and improve the fertilizer utilization rate of the current season. The product has the quick effect of a chemical fertilizer, the long effect of an organic fertilizer, bioactivity of a biofertilizer and effect enhancement of a microelement fertilizer, and also has medicinal effects of an ecological pesticide.