The invention discloses an environmentally-friendly efficient microbial compound fertilizer and a preparation method thereof. The environmentally-friendly efficient microbial compound fertilizer is prepared from chicken manure, cow dung, dried pond sludge powder, ground phosphate rock, edible fungi residues, furfural residues, a microbial agent, wheat bran, bean cakes, urea, ammonium nitrate, potassium humate, wheat straws, charcoal powder and traditional Chinese medicine residues, wherein the microbial agent is prepared from bacillus licheniformis, bacillus subtilis, bacillus mucilaginosus, bacillus megatherium, pseudomonas, bacillus thuringiensis, bacillus amyloliquefaciens and nitrogen-fixing bacteria. The edible fungi residues and the furfural residues are smashed and mixed with water, the microbial agent is added for fermentation, the Chinese traditional medicine residues are added to perform fermentation, then the rest of the raw materials are added, and the microbial compound fertilizer can be obtained by performing full mixing, granulation and drying. The raw materials used for the microbial compound fertilizer are all natural fertilizers and contain rich mineral substances, the damage of a soil acid-base structure and a nutritional ingredient structure caused by inorganic fertilizer application is avoided, and the environmentally-friendly efficient microbial compound fertilizer is greener and more environmentally-friendly.