The invention discloses a compound microbial agent, a water-soluble fertilizer containing the same and applications of the compound microbial agent and the water-soluble fertilizer. The compound microbial agent is a mixture of high organic matter yeast fermentation liquid and traditional Chinese medicine extraction waste liquid, wherein the high organic matter yeast fermentation liquid is produced through microbial fermentation and is rich in amino acid. A preparation method is simple, dispenses with aseptic conditions and is low in cost. The compound microbial agent is prepared through mixed inoculated fermentation by taking bacillus subtilis, saccharomycetes, a cold-adapted bacterium VT16 and a cold-adapted bacterium VT19 as a composite strain and utilizing the high organic matter liquid produced through fermentation and rich in amino acid and the traditional Chinese medicine extraction waste liquid as raw materials, is comprehensive in nutrients and can not only provide nutrient elements required by crop growth but also inhibit reproduction of harmful microbes. The compound microbial agent is then combined with nutrients N, P and K essential to crops, wherein the added nutrients can meet the requirements of plant growth and have high absorptivity and good absorption effects; the added microbes can conduce to inhibiting growth of plant pathogens, preventing continuous cropping diseases, promoting growth of crops and inducing plants to become resistant.