The invention discloses a composition containing a microorganism complex. The composition containing the microorganism complex comprises, by weight, 1-2 parts of Bacillus cereus, 1-2 part sof thiamethoxam and 5-25 parts of Beauveria bassiana. The pesticide composition containing the microorganism complex can be processed to prepare a wettable powder, a water-dispersible granule, a missible oil, amicroemulsion, a suspending agent or a dispersible oil suspending agent, is used for controlling pests and diseases of rice, peanut, soybean, potato, citrus, beet, rape, pepper, cucumber and eggplant,and has the use of controlling Lepidoptera, Coleoptera, Homoptera and Diptera pests, underground pests and soil-borne bacterial diseases on vegetables. The pesticide composition containing the microorganism complex can reduce the use amount of pesticides and delay the drug resistance, has a better control effect than the single doses, and reduces the cost of farmers.