The invention relates to functional organic compound fertilizer with solid organic wastes as base materials as well as a preparation method and application of the functional organic compound fertilizer. The functional organic compound fertilizer is prepared by taking the solid organic wastes as the substrate, compounding and molding the solid organic wastes with a toxic heavy metal stable complexing agent, nitrogen fertilizer, phosphorus fertilizer, potash fertilizer or manure fertilizer. The functional organic compound fertilizer is used for cultivating or maintaining crops such as trees, vegetables, flowers, grasses, wheat, millets, rice, sweet potatoes or potatoes; the solid organic wastes are kitchen wastes, garden wastes, traditional Chinese medicinal l residues, straws, fruit shells,fruit kernels, straw, bagasse, corn cobs, sawdust, paper, diapers, animal bones or shells, urban sludge, soil or coal gangue and the like. The toxic heavy metal stable complexing agent is formed by combining a secondary physical bond with the base materials, is not easy to run off and is stably complexed with toxic heavy metals in the use process; the crops are not contaminated by toxic heavy metals after the functional organic compound fertilizer provided by the invention is applied.