The invention discloses a composite wheat seed coating agent. The composite wheat seed coating agent is prepared from the following raw materials in percentage by weight: 10 to 15 percent of thiamethoxam, 0.5 to 1 percent of methylene dithiocyanate, 0.05 to 0.1 percent of growth regulator, 2 to 7 percent of dispersing agent, 1 to 4 percent of anti-caking agent, 1 to 6 percent of suspending agent, 0.1 to 3 percent of film-forming agent, 1 to 10 percent of filler, 1 to 3 percent of preservative, 0.5 to 5 percent of coloring agent and the balance of deionized water. The invention further provides a preparation method of the composite wheat seed coating agent. The composite wheat seed coating agent and the preparation method thereof provided by the invention have the beneficial effects that the seed coating agent is mainly used for coating wheat seeds; the effective components of thiamethoxam and methylene dithiocyanate are efficient degradable pesticide varieties; before wheat seeding, the seed coating agent coats wheat seeds in the pesticide-seed ratio of 1 to 50, and seeds are sown after being dried in the air in a natural state. The composite wheat seed coating agent has a remarkable control effect on wheat aphids and cyst nematode disease, can effectively lower the base numbers and disease indexes of field aphids and cyst nematodes, and has the advantages of safety, high efficiency, low toxicity, saving of labor and economic efficiency; the pesticide lasting period is prolonged, and the yield is increased by 10 percent or more.