The invention provides soil ecological system restoring organic fertilizer which is high in content of nutrients available for crops and reasonable in nutrition collocation, is thoroughly decomposed, has a small number of foreign microbes and is high in organic matter content. The soil ecological system restoring organic fertilizer comprises organic raw materials, microbial agents and NPK, wherein the organic raw materials comprise cake fertilizer, green manure, plant protein and biochemical humic acid; the microbial agents comprise nine microbial bacteria such as nitrogen-fixing bacteria, phosphorus-solubilizing bacteria, potassium-releasing bacteria, actinomycetes, saccharomycetes, lactic acid bacteria, photosynthetic bacteria, paenibacillus polymyxa and bacillus subtilis; the NPK accounts for 5-25% of the total fertilizer; the NPK comprises ammonium sulfate, ammonium chloride, ammonium nitrate phosphate, ammonium phosphate, potassium sulfate, potassium chloride, potassium nitrate, magnesium sulfate, zinc sulfate and borax; the organic raw materials are taken as the balance of the fertilizer.