As the foundation of port planning, port throughput forecasting plays a great role in determining the orientation of port development and the scale of investment. In this paper, we propose a new dynamic analysis model which combines the first-order one-variable grey differential equation model (abbreviated as GM(1,1) model) and equidimensional filling vacancies model. This combined model takes advantage of the high predictable power of GM(l,l) model and at the same time take advantage of the equidimensional filling vacancies prediction power on the discretized states based on the GM(1,1) modeling residual sequence. As an example, we use the statistical data of the throughput of Qing Huangdao port from 2000 to 2009 for a validation of the effectiveness of the improved GM(1,1) equidimensional filling vacancies model.