Abstract: Objective To establish an algorithm based on 3D convolution neural network to segment the organs at risk (OARs) in the head and neck on CT images. Methods We propose an automatic segmentation algorithm of head and neck OARs based on V-Net. To enhance the feature expression ability of the 3D neural network, we combined the squeeze and exception (SE) module with the residual convolution module in V-Net to increase the weight of the features that has greater contributions to the segmentation task. Using a multi-scale strategy, we completed organ segmentation using two cascade models for location and fine segmentation, and the input image was resampled to different resolutions during preprocessing to allow the two models to focus on the extraction of global location information and local detail features respectively. Results Our experiments on segmentation of 22 OARs in the head and neck indicated that compared with the existing methods, the proposed method achieved better segmentation accuracy and efficiency, and the average segmentation accuracy was improved by 9% . At the same time, the average test time was reduced from 33.82 s to 2.79 s. Conclusion The 3D convolution neural network based on multi-scale strategy can effectively and efficiently improve the accuracy of organ segmentation and can be potentially used in clinical setting for segmentation of other organs to improve the efficiency of clinical treatment.