Garlic root cutting is generally performed manually; it is easy for the workers to sustain hand injuries, and the labor efficiency is low. However, the significant differences between individual garlic bulbs limit the development of an automatic root cutting system. To address this problem, a deep learning model based on transfer learning and a low-cost computer vision module was used to automatically detect garlic bulb position, adjust the root cutter, and cut garlic roots on a garlic root cutting test bed. The proposed object detection model achieved good performance and high detection accuracy, running speed, and detection reliability. The visual image of the output layer channel of the backbone network showed the high-level features extracted by the network vividly, and the differences in learning of different networks clearly. The position differences of the cutting lines predicted by different backbone networks were analyzed through data visualization. The excellent and stable performance indicated that the proposed model had learned the correct features in the data of different brightness. Finally, the root cutting system was verified experimentally. The results of three experiments with 100 garlic bulbs each indicated that the mean qualified value of the system was 96%. Therefore, the proposed deep learning system can be applied in garlic root cutting which belongs to food primary processing.