The invention discloses a nitrogen, phosphorus and potassium microbial coated fertilizer and a preparation method thereof. The nitrogen, phosphorus and potassium microbial coated fertilizer comprises a pill core, a middle layer and a mycoderm layer from inside to outside in sequence; the pill core comprises the following raw materials: urea, monopotassium phosphate, diammonium phosphate, calcium superphosphate, potassium sulphate, plant ash and glutinous rice glue; the middle layer comprises the following raw materials: furfural residues, vinasse, sorghum residues, edible fungus culture medium wastes, aureobasidium pullulans, EM (effective microorganism) bacterial liquid and clay; the mycoderm layer comprises the following raw materials: peat soil, a microbial agent, Carbomer, 10 wt% sodium hydroxide aqueous solution and water. The nitrogen, phosphorus and potassium microbial coated fertilizer disclosed by the invention has a viable count of more than 0.062 billion CFU/g, an organic content of more than 60.5 wt%, a pH value of 7.1-7.2 and an N, P and K content ratio of (2-3.5):(1.5-2.1):1; the reasonable collocation is performed according to nitrogen, phosphorus, potassium and other demands of crops, so that the release period of fertilizer nutrients can be prolonged; the microbial agent improves the soil texture and the tillage performance and inhibits the emergence of weeds and pests. The preparation method of the fertilizer has the advantages that the raw materials are easy to obtain, the operation is simple, the biological survival rate is high, the activity is good, and the use effect is outstanding.