The spectrum of self-made staining in cigarette and actual staining in cigarette spots were collected by attenuated (ATR-FTIR). Through the methods of intuitive comparison, database retrieval and similarity calculation, the sources of cigarette pollution were analyzed. And the Bootstrap method was used to set the similarity threshold, and the identification model of the staining in cigarette pollution source was established. The results showed that the method could verify the correct rate of the sample with 100%, and realize the qualitative analysis of the source of the staining in cigarette pollution. The method has good precision and reproducibility, and the RSD is less than 0.01% (n=5). The method can accurately detect the cause of the actual staining in cigarette, and is suitable for the detection of the source of the staining in cigarette.