Abstract: Cotton (Gossypium hirsutum) is one of the most important cash crops in China, The timely and effective removal of weeds in cotton seedling stage is an important measure to ensure high and stable yield of cotton. Nowadays, weed recognition based on machine vision is widely used. The fast and effective recognition of crop and weed in the field under natural illumination is one of the key technologies for the development of intelligent mechanization weeding pattern. In the one hand, cotton and weeds have similar color feature in the field. Feature presentation of the natural property of target is difficult to be obtained by the hand-engineered feature extractor. The spatial consistency of the obtained features is not good, and the real-time performance of recognition system is reduced for the complex feature extraction algorithm. On the other hand, the effect of image preprocessing has important influence on recognition results. In order to solve the main problems in the current research, we explored the way to improve the recognition accuracy, stability and real-time performance, and a recognition method of crop and weed based on Faster R-CNN．In this paper, cotton seedling at 2-5 leaves stages and weeding during the same stage were used as research objects under natural illumination. Weed identification from digital images taken under natural illumination at field level is still challenging in agricultural image processing applications, though a lot of research has been conducted related to this topic. To address this problem, images including cottons and weeds were taken vertically from top to bottom. A method based on Faster R-CNN convolutional neural network was proposed to identify weeds from cotton plants more accurately and quickly. The residual network was used to extract image features, with ReLU as the activation function and Max-pooling as the down-sampling method. In the region of proposal network, feature pyramid network was introduced to generate target candidate frame, and Softmax regression classifier was utilized to optimize the CNN network. The proposed methodology was implemented on 200 digital images taken under natural illumination. The experimental results demonstrated that, the average accuracy of weed identification reached 95.5%, and the average time for individual weed plant identification was 1.51 s, which was reduced to 0.09 s by using GPU. To test the efficiency of the proposed methodology, YOLOv3 method was also carried out on the same training and test datasets. The weed identification results were assessed by mean average precision and average precision. The experimental results showed that better performance was achieved by using our proposed methodology, and better identification accuracy was reached as well. This indicated that the proposed method had a good effect on weed detection under natural illumination, and it will greatly promote the development of precise weed control.