The invention relates to a microbial composite water purifying agent. The microbial composite water purifying agent is composed of a composite microbial preparation and a water purifying agent composite carrier, wherein the composite microbial preparation comprises bacillus subtilis, bacillus amyloliquefaciens, lactobacillus acidophilus, bacillus coagulans, bacillus licheniformis and pseudomonas aeruginosa; the water purifying agent composite carrier comprises polyacrylamide, polyaluminum ferric chloride, polyether quaternary ammonium salt, diatom ooze, coconut shell charcoal, chitosan, sulfonated coal, zeolite, clay and hydroxyapatite. The microbial composite water purifying agent adopts indigenous microorganisms in river and lake water bodies and bottom mud, and is rich in resource, easyto obtain and low in cost; the indigenous microorganisms subjected to enlarged culture are rapidly propagated and can be cooperated with the water purifying agent to degrade a large amount of pollutants in water, so that a carbon source is converted into carbon dioxide, a nitrogen source is converted into nitrogen, the pollutant concentration is greatly reduced, and the water body becomes clear.