Grape shelf-life estimation is a substantial challenge for the grape industry. The objective of this study is to investigate the potential of grape shelf-life estimation using HSI technique and a deep learning algorithm. The visible and near-infrared (400.68–1001.61 nm) hyperspectral reflectance images data of grape samples was acquired and preprocessed with different spectral preprocessing methods. Additionally, a stacked denoising autoencoder (SDAE)-based deep learning algorithm was developed to extract deep features from pixel-level hyperspectral data of grapes, and then these features were used as inputs to establish support vector machine (SVM) models for estimating grape shelf-life. Furthermore, SVM, one-dimensional convolutional neural network (1D CNN) and long short-term memory (LSTM) models were used as traditional machine learning and end to end models for comparison. The results demonstrated that the SDAE-SVM model achieved reasonable recognition accuracy of 100 % and 98.125 % for the shelf-life of grapes in the training and test sets, respectively. The overall results suggested that SDAE-based deep learning method can be used as a powerful tool to deal with large-scale hyperspectral data as well as this research confirms the feasibility of non-destructive estimation for grapes shelf-life by the combination of HSI technique and deep learning method, which would provide a valuable guidance for shelf-life estimation of other postharvest fruit.