Chrysanthemum is derived from the capitulum of Chrysanthemum. Chuju, Gongju, Hangju and Boju are common medicinal chrysanthemums. Different chrysanthemum varieties have great similarities in appearance, and it is difficult for laypeople to identify them accurately only by naked eyes. The conventional instrumental analysis method has the disadvantages of high detection cost, long analysis time, and destructive treatment of samples, which affects the secondary sales of the products. As a green, simple and rapid detection technology, near-infrared spectroscopy has made great progress in traditional Chinese medicine identification. This study established a nondestructive identification method of different Chrysanthemum varieties based on portable near-infrared spectrometer and chemometric methods. The spectra of complete and powder samples of Chuju, Gongju, Hangju and Boju were collected by grating portable near-infrared spectrometer. The single and combined spectral pretreatment methods were used to eliminate the interferences in the spectra. The identification models of different Chrysanthemum varieties were constructed by combining principal component analysis, soft independent modeling of class analogy and Fisher linear discriminant analysis methods. The results show that: due to the restrictions of the current measure instruments and the difference of sample particle size and distribution, there are obvious interferences of background, baseline drift and noise in the spectra. The baseline drift interference is particularly serious for the analysis of the complete samples. The principal component analysis combined with spectral pretreatment methods could not identify different varieties of chrysanthemum. The best identification accuracy of complete samples was only 8.33%, and that of powder samples was 52.38%. The soft independent modeling of class analogy can obtain more accurate identification results with preprocessing methods. The identification accuracy of complete sample data is 95% with first derivative+multiple scattering correction, while the identification accuracy of powder sample data is 92.5% with the original data. The results of Fisher linear discriminant analysis are the best. When the complete sample spectra were optimized by continuous wavelet transform, the identification accuracy was 97.5%. When the original spectra of powder samples were used, the identification accuracy could reach 100%. The above results show that the complete and powder samples’ identification results are consistent when the appropriate pretreatment and modeling methods are used. Based on the grating portable near-infrared spectrometer combined with chemometrics methods, the accurate identification of different Chrysanthemum varieties can be realized, which provides a new way for the nondestructive identification of food and drug homologous products.