Proper identification of different grape varieties by smart machinery is of great importance to modern agriculture production. In this paper, a fast and accurate identification method based on Canonical Correlation Analysis (CCA), which can fuse different deep features extracted from Convolutional Neural Network (CNN), plus Support Vector Machine (SVM) is proposed. In this research, based on an open dataset, three types of state-of-the-art CNNs, seven species of deep features, and a multi-class SVM classifier were studied. First, the images were resized to meet the input requirements of a CNN. Then, the deep features of the input images were extracted by a specific deep features layer of the CNN. Next, two kinds of deep features from different networks were fused by CCA to increase the effective classification feature information. Finally, a multi-class SVM classifier was trained with the fused features. When applied to an open dataset, the model outcome shows that the fused deep features with any combination can obtain better identification performance than by using a single type of deep feature. The fusion of fc6 (in AlexNet network) and Fc1000 (in ResNet50 network) deep features obtained the best identification performance. The average F1 Score of 96.9% was 8.7% higher compared to the best performance of a single deep feature, i.e., Fc1000 of ResNet101, which was 88.2%. Furthermore, the F1 Score of the proposed method is 2.7% higher than the best performance obtained by using a CNN directly. The experimental results show that the method proposed in this paper can achieve fast and accurate identification of grape varieties. Based on the proposed algorithm, the smart machinery in agriculture can take more targeted measures based on the different characteristics of different grape varieties for further improvement of the yield and quality of grape production.