The work aims to develop a new method for classifying paper cup evidences. Thirty-one disposable paper cups from different manufacturers were tested through X-ray fluorescence spectrometry. Meanwhile, for spectral data, two main factors containing 79.209% of the information of the original spectral data were determined by factor analysis. Four factor analysis models and factor score functions were established with the two main factors so as to calculate the factor score, and then the original data were replaced by factor scores for systematic clustering. Finally, Fisher's discriminant analysis was performed to verify the accuracy and reasonableness of the clustering results. When 31 disposable paper cup samples were divided into three categories, the disposable paper cup samples of the same company were grouped into one category. The samples had good discrimination, and the classification accuracy was 100%. By means of X-ray fluorescence spectrometry, factor analysis and systematic clustering, the nondestructive, rapid and effective inspections as well as classification of different paper cups can be achieved with accurate and reliable results.