The quality of port service system may have an impact on the shipper’s port selection behavior or even an influence on the cost of the whole fleet, so port choice is an important part of transportation demand behavior analysis. Statistical analysis, analysis of variance, and multivariate analysis are commonly used analysis methods in port selection. In addition to traditional used analysis method, we apply the grey theory (grey relational analysis and grey cluster analysis) to port selection in this study. The results of our study show that both the traditional used methods and the grey theory provide a good and consistent result. The main difference between the commonly used methods and the grey theory is in that the latter can deal with incomplete information, and uncertain causality, and also can provide a good result. The difference mentioned above is also the main advantage of the grey theory.