The invention discloses a complex acidophilic microbial agent, wherein the colony consists of five strains, namely ferroplasma thermophilum, leptospirillum ferriphilum, sulfobacillus thermosulfidooxidans, acidithiobacillus ferrivorans, acidithiobacillus ferroxidans and the like. The preparation method of the complex microbial agent sequentially comprises steps of proportional compounding of microbial agent, temperature gradient complex culture, waste copper-clad plate residue tolerance domestication and the like; and by virtue of the complex acidophilic microbial agent disclosed by the invention, valuable metallic copper in high-grade or low-grade waste copper-clad plate residue can be leached, which can be specifically achieved by an operating process as follows: mixing the complex microbial agent with waste copper-clad plate residue and iron-containing basic salt/nutrient medium so as to obtain mixed slurry; and continuously stirring and leaching at room temperature until a leaching operation is completed, and meanwhile ventilating in the bottom. The complex microbial agent and the application thereof disclosed by the invention have the advantages of being simple in formula, good in economical efficiency, strong in adaptability, efficient and the like.