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The paper takes National Topographic Database by assuming vector diagram water system with 1:250,000 scale as a data source. A reasonable and efficient coding method for river network is presented, which can solve the coding problem of converged river network, bifurcate river network, crossed river network and water of lake and reservoir. The coding method can reflect the topology of river network and can locate any stream segment of river network directly and operate the topology of river network effectively. At the last, this coding method is applied to parts of stream segments in Taihu Lake basin. As the results, the coding method is made by the paper can solve the coding problem of complicated river network, the upstream-downstream relationship can be easily identified through the coding of stream segment, the self-replicating coding has excellent expansibility and high efficiency, and can be handled easily by the computer.