Citri Reticulatae Pericarpium (CRP), has been used in China for hundreds of years as a functional food and medicine. However, some short-age CRPs are disguised as long-age CRPs by unscrupulous businessmen in order to obtain higher profits. In this paper, a rapid and nondestructive method for the classification of different-age CRPs was established using portable near infrared spectroscopy (NIRS) in diffuse reflectance mode combination with appropriate chemometric methods. The spectra of outer skin and inner capsule of CRPs at different storage ages were obtained directly without destroying the samples. Principal component analysis (PCA) with single and combined spectral pretreatment methods was used for the classification of different-age CRPs. Furthermore, the data were pretreated with the PCA method, and Fisher linear discriminant analysis (FLD) with optimized pretreatment methods was discussed for improving the accuracy of classification. Data pretreatment methods can be used to eliminate the noise and background interference. The classification accuracy of inner capsule is better than that of outer skin data. Furthermore, the best results with 100% prediction accuracy can be obtained with FLD method, even without pretreatment.