Wuyuan green tea is a famous agricultural product in China and a product protected by national geo-graphical indications. The processed green tea also needs to remove impurities, such as stones, tea stalks, etc. However, tea stalks cannot be classified from Wuyuan green tea using photoelectric sorting and 2D image recognition technology since they have similar colors. This paper adopts hyperspectral imaging technology to solve the problem of inaccurate sorting caused by their similar colors. Green tea containing tea stalks was imaged using a visible and near-infrared camera with a wavelength of 400nm-1000nm. What’s more, Principal Component Analysis (PCA) was adopted to reduce the dimension of the col-lected hyperspectral image. And the Convolutional Neural Network (CNN) was used constructively to identify tea stalks in hyperspectral image, the CNN can automatically learn the corresponding features, avoid the complex feature extraction process. The experimental results showed that the recognition accuracy for tea stalks reaches 98.53%. The method has a high recognition rate and can meet the actual production requirements. After field testing, the selection rate is as high as 97.05%.