The present disclosure is directed to a computer-implemented method and system for anatomical tree structure analysis. The method may begin with receiving a task of the anatomical tree structure analysis. Then, a set of positions in the anatomical tree structure may be set or received, by a processor, as the sampling positions for model inputs and model outputs. Then model inputs may be determined, by the processor, at the sampling positions on the basis of the task. An encoder may be selected, by the processor, for each position of the set of positions on the basis of the task. The encoder may be configured to receive a model input at each position and extract features for the corresponding position. After that, a tree structured recurrent neural network (RNN) may be constructed by the processor with nodes corresponding to the set of positions and connected with the respective encoders. An RNN unit for each node may be selected on the basis of the task and an information propagation among the nodes may be set on the basis of the spatial constraints of the set of positions in the anatomical tree structure. The generated treed structured RNN may be provided for performing the task of the anatomical tree structure analysis.