The invention discloses a composite microbial preparation for treating watercourse organic matter. The composite microbial preparation is prepared from the following ingredients in percentage by weight: 10 to 20% of pseudomonas, 10 to 15% of vibrio, 10 to 15% of flavobacterium, 10 to 15% of pure nitrite coccus, 10 to 15% of thiobacillus thiooxidant, 10 to 20% of bacillus subtilis, 5 to 15% of bacillus licheniformis, 5 to 10% of aneurinibacillus aneurinilyticus, 5 to 10% of saccharomycetes, 5 to 10% of micrococcus denitrificans and 5 to 10% of actinomycetes. Compared with the prior art, the composite microbial preparation disclosed by the invention can rapidly decompose organic wastes, and effectively inhibits growth of harmful microorganisms; when the composite microbial preparation is put into polluted water, by utilizing metabolic activity of the microorganisms, concentration of pollutants in the water is reduced, the problems of blackening and smelliness of the water can be obviously improved, ammonia nitrogen content and total phosphorus content in the water are reduced, harmful substances such as hydrogen sulfide are decomposed, the water environment is improved, and transparency of the water is obviously improved; the composite microbial preparation has the advantages of simplicity for preparation, low cost and application to watercourse treatment, and has great economic and environmental-friendly significance for watercourse treatment.