The invention relates to a flocculating agent for simulating composition of microorganism extracellular polymeric substances and an application method thereof. The flocculating agent is formed by compounding microorganism exopolysaccharides (sodium alginate, xanthan gum and pulullan) and hydrophobic amino acid (tryptophan, tyrosine and phenylalanine), the weight ratio (ammonia acid/polysaccharide) is 2-8, the optimal ratio is 8, and the concentration of the flocculating agent in the system when in charging is controlled at 20-40mg/L. The flocculating agent has the characteristics that the bridging attraction effect of the exopolysaccharide and the hydrophobic attraction effect of the hydrophobic amino acid can be adequately played after all components are compounded, so that the formation of non-biological particle sludge in the heavy metal waste water treatment process can be effectively promoted by integrating the bridging attraction effect and the hydrophobic attraction effect. Compared with the flocculent sludge, the flocculating agent has the advantages that the settleability of the non-biological particle sludge can be increased by 2-5 times, and the weakness of the difficulty in solid-liquid separation in the heavy metal waste water treatment process and toxicity and harm of the traditional macromolecular flocculating agent can be overcome.