Abstract: Ports play an important role in transporting system in China, which have significant influence on regional economy development. Indexes Analysis and Zipf's law were used to measure the difference of regional and the change of hierarchical size structure in scale of large-capacity ports from 1995 to 2013. The results showed that port throughput in China rapidly increase, and foreign trade exportation is dominant in the development. Theil Index and Herfindahl-Hirschman Index analysis showed that the throughput gap between regional ports decrease, and port primary index analysis indicated that difference of hierarchical size structure becomes narrow. Large-capacity port throughput have rank-size distribution, and fractal structure is change from single fractal to double fractal, Zipf parameter of these ports decrease. Grey relativity analysis showed that the main factors of port throughput are diverse in different provinces, and these provinces can be divided into four styles, which including regional pull, extroverted economy, hinterland transformation and supplementary orientation.