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The study uses the carbon dioxide emission calculation model published by IPCC to measure carbon dioxide emissions and fuel inputs of the three types of multimodal transport (road-sea, railway-sea, and river-sea) in ports of China. Then, we make a case study on Shanghai port. Combined with carbon taxes launched around 2012 in China, this paper calculates the carbon taxes on the three types of multimodal transport and makes a pairwise comparison between roadway/railway, roadway/waterway and waterway/railway. The results show that increasing the proportion of railway-sea transportation and river-sea transportation to a reasonable level will achieve great energy saving, emission reduction, and economic benefits. According to different transportation network features, this paper applies Cluster analysis to raise separately suggestions for long-term development of coastal container ports in China based on low-carbon thinking.