The present disclosure is directed to a method and device for generating anatomical labels for a physiological tree structure. The method may include receiving a 3D model and a 3D skeleton line of the physiological tree structure. The 3D model is restructured based on medical image data of the physiological tree structure acquired by an imaging device. The method further includes selecting at least one level from extracting geometrical features from a pool of selectable levels. The method also includes extracting, by a processor, geometrical features from the 3D model of the physiological tree structure along the 3D skeleton line at the selected at least one level. The method also includes generating, by the processor, anatomical labels for the physiological tree structure using a trained learning network based on the extracted geometrical features.