The present invention discloses a pesticide compound agent for preventing and treating onion root rot, and a screening method thereof. According to pathogenic bacteria of the onion root rot and characteristics of the pathogenic bacteria, a bacteria type and pesticide combination compounding manner is selected for preventing and treating the onion root rot by isolation and identification of bacteria, biological determination, and screening of agents and compound agents. The pesticide compound agent comprises effective component of a trichoderma harzianum and thiram compound agent or a trichoderma harzianum and carbendazim compound agent; the relative preventive effect of the trichoderma harzianum and thiram compound agent is 92.41%, and the relative preventive effect of the trichoderma harzianum and carbendazim compound agent is 76.74%, so that the preventing and treating effect on the onion root rot is obvious. In the present invention, manners that the bacteria are treated by corresponding bacteria, and bacteria and bactericide are combined and adopted to realize preventing and treating of the onion root rot; in the preventing and treating processes, pesticides are low in toxicity, long in acting time and low in environmental pollution level.