The invention discloses a fertilizer-pesticide double-effect double-chelated multi-element multi-functional medical stone liquid fertilizer and a preparation method thereof. The liquid fertilizer is prepared by compounding and mixing raw powder of medical stones, soluble silicon, limestone, compound amino acid, ammonium phosphate, urea, potassium oxide, magnesium sulfate, ferrous sulfate, manganese sulfate, copper sulfate, boracic acid, zinc sulfate, ammonium molybdate, selenium powder, poly(potassium aspartate) and the like, a botanical pesticide composition agent prepared from ricin, veratrine, herba asari volatile oil, rotenone, clausena dunniana essential oil, coptis chinensis alkaloid and glycyrrhizic acid, an amino-oligosaccharin bacteriostatic agent, gibberellin, alum, DA-6, EDTA, hydrochloric acid, ethyl alcohol and the like. The preparation method of the liquid fertilizer comprises the steps that the raw materials are mixed and compounded to generate a hot-melting reaction with aqueous diluted hydrochloric acid, the materials and urea are added with water, mixed dissolving is conducted by increasing the temperature to 100 DEG C, then the reactants and the botanical pesticide composition agent are diluted, mixed, compounded and foamed to be mixed with synergistic liquid, the materials are heated until the temperature is 80 DEG C to 120 DEG C and dissolved and mixed, solid-liquid separation is conducted to remove residues, the obtained liquid is delivered into the reaction kettle to be subjected to secondary chelation with EDTA and DA-6, and then the high-concentration suspension type liquid fertilizer is prepared in a mixed mode.