In order to quickly identify the adulteration in lily, pure lily and adulterated lily were analyzed by excitation-emission matrix (EEM) fluorescence spectroscopy technique, and the fluorescence fingerprints of lily and adulterated lily were constructed. Then, two chemical pattern recognition methods, namely principal component analysis linear discriminant analysis (PCA-LDA) and partial least squares discriminant analysis (PLS-DA), were used to identify and classify the adulterated powder of lily. The experimental results show that both two classification models can accurately identify adulterated lily samples using EEM fluorescence spectrum data, and the correct classification rates (CCRs) of both models are above 95%. Using PCA-LDA and PLS-DA, new methods for rapid identification of lily adulteration were successfully established, and the fluorescence fingerprint of lily was improved, which is expected to lay a foundation for establishing a more comprehensive and accurate quality standard system for evaluating lily.