The invention provides an acidic soil conditioner, and a preparation method and application thereof. The acidic soil conditioner comprises the following components in part by weight: 4 to 8 parts of composite bacterial agent, 80 to 90 parts of acid adjusting factor, 3 to 7 parts of chelate and 2 to 6 parts of organic matter. The acidic soil conditioner adjusts the pH value of soil, promotes formation of soil aggregate structures, improves the physical property of the soil, creates a good ecological environment for the growth of plants, increases organic matters, calcium, magnesium and silicon and the activities thereof, promotes healthy growth of crops, enhances stress resistance and prevents diseases and pests. By adoption of the composite bacterial agent, the constitution of a microflora of the soil can be improved, the microbial activity of the rhizosphere of the crops is enhanced, mineralization of organic pollutants is accelerated, growth of the plants is promoted, and absorption of degradation products and bioremediation of the polluted soil are accelerated. The acidic soil conditioner has no toxicity, residues and pollution, accords with the development tendency of organic pollution-free agriculture and has great popularization and application values.