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China has very long coastline and many large navigable rivers, and with the rapid process of Chinese industrialization, Water transport has played more and more important role in transport and logistics system in recent years. One regularity phenomenon appears apparently in China: the more developed one region in economy, the more enough its water transport is utilized. At present, the scalar imbalance development of water transport is very similar to the economic level differences among different regions in China. Based on four importance indices of water transport, the paper analyzes and classifies the water transport of 31 provinces and municipalities except Taiwan, Hongkong and Macao of China through principal component and clustering analysis method, and further explores some bottlenecks that some regions with good conditions of water transport have no gotten enough development.