The invention discloses a disinfectant composition of percolate for rotting a discomfort tobacco. The disinfectant composition is prepared from a sodium dichloro cyanurate industrial product of which the active chlorine content is greater than 50% and a dioctadecyl dimethyl ammonium bromide industrial product of which the content of an active substance is greater than 90%. The percolate generated in a process of rotting the discomfort tobacco is sterilized and directly scattered according to the fact that the ratio of the disinfector to the percolate is 1 to 15-300; the tobacco mosaic virus (TMV) can be effectively killed, and the inactivation ratio is more than 98%. The disinfectant composition has the characteristics that the raw material is easy to obtain, the process is simple, and the composition is environment-friendly and harmless to a human body. The disinfectant composition is suitable for popularization and application in a tobacco growing area, and secondary infection of the percolate with the tobacco mosaic virus caused by rotting of the discomfort tobacco on crops such as tobacco in the next season is avoided.