Studying the coordination of varied freight modes from the perspective of geographic regions is conducive to understanding the regional differences, and this can provide effective countermeasures and suggestions for the sustainable and coordinated development of freight transport. To reflect on the effects of regional differences in the coordination of freight modes, we divided China into four regions: The East, Central, West, and Northeast. We examined freight mode coordination in terms of region and analysed the coordination of freight modes from three aspects: one within a single freight mode system, between varied freight modes, and among freight modes and the economy in different regions. We selected 19 freight indexes based on China’s freight data from 2008 to 2017, and determined the relationship between the freight index and economic index gross domestic product (GDP) growth rate by means of stability, co-integration, and the Granger causality test. The coordination models within a single freight mode and among varied freight modes were established, and we conducted spatial autocorrelation between the freight mode and the economy. The results demonstrated that in the four regions of China, the single-freight mode had coordination of over 0.80; the coordination between waterway and aviation freight transport was over 0.83; and the coordination of varied freight modes in the Eastern region exceeded 0.78, with good overall coordination. Among the four regions, the spatial correlation between the Eastern and Western regions was not significant, while the correlation between the Central and Northeast regions was significant. The model and analysis methods established in this study were feasible and effective. In view of the universality of the model, it can be easily applied and generalized in or out of China.