The geographical origin and the important nutrient contents greatly affect the quality of red raspberry (RRB, Rubus idaeus L.), a popular fruit with various health benefits. In this study, a chemometrics-assisted hyperspectral imaging (HSI) method was developed for predicting the nutrient contents, including pectin polysaccharides (PPS), reducing sugars (RS), total flavonoids (TF) and total phenolics (TP), and identifying the geographical origin of RRB fruits. The results showed that these nutrient contents in RRB fruits had significant differences between regions (P < 0.05) and could be well predicted based on the HSI full or effective wavelengths selected through competitive adaptive reweighted sampling (CARS) and variable iterative space shrinkage approach (VISSA). The best prediction results of PPS, RS, TF, and TP contents were achieved with the highest residual predictive deviation (RPD) values of 3.66, 3.95, 2.85, and 4.85, respectively. The RRB fruits from multi-regions in China were effectively distinguished by using the first derivative-partial least squares discriminant analysis (DER-PLSDA) model, with an accuracy of above 97%. Meanwhile, the fruits from three protected geographical indication (PGI) regions were successfully classified by using the orthogonal partial least squares discrimination analysis (OPLSDA) model, with an accuracy of above 98%. The study results indicate that HSI assisted with chemometrics is a promising method for predicting the important nutrient contents and identifying the geographical origin of red raspberry fruits.