The invention discloses a compound microbial fertilizer and a preparation method and application thereof. The compound microbial fertilizer is prepared from, by weight, 1%-2.5% of bacillus megatherium, 2%-3.5% of salt decomposing bacteria, 0.5%-1% of bacillus subtilis, 0.5%-1% of bacillus licheniformis, 0.5%-1.5% of bacillus amyloliquefaciens, 1%-3.5% of bacillus mucilaginosus, 6%-8% of nitrogen, phosphorus and potassium, 1%-3% of medium trace elements, 10%-25% of amino acid powder, 30%-55% of humic acid and 8%-20% of moisture, wherein the proportion sum of all the components contained in the compound microbial fertilizer is 100%. According to the compound microbial fertilizer, saline-alkali lands can be neutralized, the physicochemical properties of saline-alkali soil and the soil structure can be improved, the permeability can be improved to accelerate salt leaching, the utilization ratio of the medium trace elements can be increased, and the desalting effect is good; meanwhile, nitrogen, phosphorus and potassium and multiple microorganisms are added, the soil fertility is improved, decomposition of matter difficult to decompose is accelerated, soil-borne diseases are inhibited, and successive cropping obstacles are overcome.