The invention relates to a method for preparing a special fertilizer by treating kitchen waste, sludge and domestic waste in one machine, which comprises the following steps: while sending domestic waste organic substances into a pulping machine, adding slurry, which is obtained by separating out nondegradable substances from the kitchen waste and crushing, and a proper amount of water from a feed port of the machine in a water addition mode, mixing the two wastes into fine uniform slurry, adding the sludge, and evenly stirring; and removing heavy metals, decomposing dioxin, carrying out microbial deep anaerobic fermentation, dehydrating, blending with material with bacteria, fermenting by high-temperature mineralization reaction, and carrying out a double-coordination production technique to produce the microbial organic fertilizer. The invention is beneficial to protecting and improving the ecological environment, can provide a high-quality fertilizer for agriculture, obviously improves the soil, enhances the crop yield and quality, and supports the sustainable development of agriculture. The invention is not only suitable for big cities, but also more suitable for medium and small cities and counties where the quantities of kitchen waste and sewage treatment plant sludge are small and independent treatment for kitchen waste and sludge is not cost-effective economically.