The invention discloses a pesticide composition containing a thiosulfonic acid ester fungicide. The pesticide composition contains 10-60% of thiosulfonic acid ester, powders of 1-40 parts of methoxy-crylic acid fungicide, a soluble concentrate, a microemulsion, an emulsion in water, a suspending agent or missible oil. The pesticide composition is a compound composition of the thiosulfonic acid ester fungicide and the methoxy-crylic acid fungicide, high synergetic effect can be generated, and the capabilities of sterilization, disease prevention and healing can be reinforced, so that the crop can be prevented from falling ill in the growth process, and the yield and the quality are improved; the pesticide composition has a broad-spectrum sterilization capability, can prevent the diseases caused by various germs, and particularly plays the role of forcefully killing the moulds; and according to the pesticide composition, the use dose is reduced relatively, and the using cost is lowered relatively; the pesticide composition is processed to be a water-based environment-friendly agent, such as the emulsion in water, the microemulsion, a suspending agent and a suspension emulsion, the use dosage of the organic solvent is reduced, and the safety of the pesticide composition is improved.