The present disclosure relates to a method and a system for generating anatomical labels of an anatomical structure. The method includes receiving an anatomical structure with an extracted centerline, or a medical image containing the anatomical structure with the extracted centerline; and predicting the anatomical labels of the anatomical structure based on the centerline of the anatomical structure, by utilizing a trained deep learning network. The deep learning network includes a branched network, a Graph Neural Network, a Recurrent Neural Network and a Probability Graph Model, which are connected sequentially in series. The branched network includes at least two branch networks in parallel. The method in the disclosure can automatically generate the anatomical labels of the whole anatomical structure in medical image end to end and provide high prediction accuracy and reliability.