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The invention relates to the technical field of compound fertilizers, and provides a high-temperature-resistant bacteria-containing compound fertilizer and a preparation method thereof.The preparation method comprises the following steps that nanoscale freeze-dried bacterial powder is prepared from bacillus, bacillus stearothermophilus and rhodopseudomonas palustris; mixing the nano TiO2 modified SiO2 composite aerogel, diatomite, the modified charcoal, sepiolite and pullulan to prepare a microbial inoculum protection composite carrier; and mixing the freeze-dried bacterial powder with a carrier, and drying to obtain the micron-sized capsule bacterial agent. Uniformly mixing a reinforcing agent, a plasticizer and a stabilizer to prepare a performance regulator; the preparation method comprises the following steps: melting choline chloride-containing urea and monoammonium phosphate to prepare molten slurry; mixing the molten slurry with a compound fertilizer to form uniform slurry; and mixing the slurry with a micron-sized capsule microbial inoculum and a performance regulator, and granulating to obtain the high-temperature-resistant bacterium-containing compound fertilizer. By optimizing the adaptability of a microbial agent embedding carrier and a melting system, the technical bottleneck of conflict between high-temperature inactivation of the microbial agent and physical properties of a product is solved.