The invention discloses a compound microbial preparation as well as a preparation method and application thereof. The preparation comprises phanerochaete chrysosporium balls, polyvinyl alcohol, silicon dioxide, activated carbon, sodium alginate and zeolite powder, which form the compound microbial preparation through crosslinking by a solution with sodium dihydrogen phosphate. The preparation method comprises the steps of preparing a gel liquid with the polyvinyl alcohol, sodium alginate, silicon dioxide and zeolite powder, mixing with a phanerochaete chrysosporium spore suspension with the activated carbon, then gradually dripping into the solution with the sodium dihydrogen phosphate so as to prepare embedded balls, and cultivating by a Kirk inorganic culture solution so as to prepare the compound microbial preparation. The compound microbial preparation has many gaps, high adsorption efficiency and good selectivity, the adsorbent has strong stability, the preparation method has the advantages of simple operation, low cost, affordability and so on, and the compound microbial preparation can be used for eliminating cadmium and 2, 4-dichlorophen in waste water.