The invention discloses an agricultural ecological probiotic composite microbial inoculant which is composed of Bacillus, Acinetobacter, Trichoderma reesei, Candida tropicalis, Lactobacillus rhamnosus, Clostridium butyricum, photosynthetic bacteria, pseudomonas fluorescens, trichodermin, Paracoccus denitrificans, a carrier and a protective agent. The effective viable count of each strain is greater than 10<6>/g. By screening multiple non-antagonistic microbial strains to establish the dominant flora, the agricultural ecological probiotic composite microbial inoculant can avoid soil-borne diseases, overcome the continuous cropping obstacle, restore the soil organism ecological balance, effectively regulate the soil pH, eliminate hardening and enhance the soil activity, stress tolerance and soil fertility. The agricultural ecological probiotic composite microbial inoculant decomposes and activates major, minor, trace and other water-insoluble low-absorptivity nutrient elements in soil, increases the absorptivity of crops for nitrogen, phosphorus and potassium, greatly enhances the fertilizer efficiency, lowers the pesticide consumption, improves the quality, appearance and flavor of the agricultural products, effectively degrades agricultural residues and lowers the chemical damage.