Taking Shanghai port as an example, this paper discusses the variaton characteristics of port throughput by the empirical mode decomposition method. It is found that the variation of Shanghai port’s cargo throughput has the periods of 3~4 months, quasi 6 months, quasi 1 year, quasi 2 years and quasi 6 years. These variation characteristics are related to the fluctuation cycle of the social production and consumption, national economy grow, macro-control, international trade and economic fluctuations, etc. Finally, the instructive significance of the mode decomposition to the practical work is discussed.