The invention discloses a method for producing a functional microorganism organic fertilizer by using food residue. According to the invention, the food residue is subjected to solid-liquid separation, and solid residue and liquid residue are respectively recycled, therefore, the cost for purchasing a culture medium when a strain is cultured is saved, the food residue is fully and maximally utilized without generating secondary pollution. For first-time fermentation of a fermentation substrate, inoculation of a large quantity of beneficial bacteria is adopted, and the beneficial bacteria are immediately propagated in short time and dominate in the fermentation substrate to play a role of sterilizing, therefore, the energy consumption and input required by sterilization are reduced, and the time of decomposing the substrate thoroughly is shortened. During secondary fermentation, a special functional strain is selected and applied to play roles in preventing, resisting and treating diseases of plants, and therefore the additional value of a product is fully developed. The method is used for reasonably and thoroughly treating the food residue and producing the functional microorganism fertilizer with strong practicability and high value by using the functional strain, maximizes the use values of food residue and is environment-friendly.