The invention belongs to the technical field of agricultural fertilizers, and particularly discloses a nitrogen-fixing microorganism compound fertilizer and a preparation method. The nitrogen-fixing microorganism compound fertilizer comprises polypeptide urea, a phosphatic fertilizer, polypeptide chelating potassium, a compound microorganism agent, a polypeptide compound, a soil conditioner, a medium trace element compound and a nutrition agent; the compound microorganism agent contains nitrogen-fixing bacteria, phosphate solubilizing and potassium solubilizing bacteria, photosynthetic bacteria, probiotics and adsorbate. The preparation method disclosed by the invention comprises the steps of preparing compound microorganism agent fermentation liquor, mixing the fermentation liquor with the adsorbate uniformly and preparing the compound microorganism agent and a microorganism envelope complex agent successively; mixing the microorganism envelope complex agent, a humic acid envelope organic fertilizer and a polypeptide envelope inorganic fertilizer uniformly, under the action of an electric field and a magnetic field, adding medium trace elements, spraying bone glue, and preparing nitrogen-fixing microorganism compound fertilizer particles. The compound fertilizer disclosed by the invention has the effects of adjusting nutrients, stimulating crop growth, improving the agricultural product quality, increasing yield and efficiency, preventing insect diseases, increasing soil fertility, loosening and improving soil quality and the like.