The invention discloses a hydrological dependent structure modeling method based on mutual information and vine copula. Firstly, mutual information and conditional mutual information are used to measure the correlation and uncertainty of hydrological variables, in combination with the principle of the strongest correlation and the least uncertainty, the structure of vine copula is selected, starting from the first tree, the mutual information of pairs of paired variables is calculated, the pairing mode that maximizes the sum of mutual information is selected as the edge of the tree, the conditional mutual information of possible pairing variables is calculated, and the pairing mode that maximizes the sum of conditional mutual information is selected as tree 2, and the pairing mode is repeated until the structure of the whole tree is determined. Secondly, according to the tree structure, fitting of edge distribution is carried out, a goodness-of-fit test is carried out, starting from tree 1, the AIC criterion is utilized to determine the copula type of the edge, parameters are estimated, a goodness-of-fit test is performed, then the conditional edge distribution of variables is calculated, and the determination of copula type, estimating parameters and testing steps are repeated until all the trees are determined. All trees and edges are connected to complete the modeling of hydrological dependent structures.