Abstract: In order to fully adapt to scenario of container multimodal transportation in the Yangtze River, on the basis of analyzing the characteristics of such scenario, the impact of uncertain freight rates and navigation conditions of different route segments are taken into account in this paper. A route optimization model for container multimodal transportation in the Yangtze River with uncertain conditions is built with the objective of minimizing the total cost including transportation turnover cost, carbon emission cost and time cost. Also, a Monte Carlo simulation and an improved wolf colony algorithm are designed to solve the model. Finally, an example is given to verify the effectiveness of the improved wolf colony algorithm. The analysis results of the example show that highway transportation can effectively control the time cost of transportation, while railway and waterway transportation have more advantages in transportation economy and greenness. Considering the navigation capacity and the maximum number of transfers of the Yangtze River waterway, the transportation task may choose a transportation scheme with higher cost to meet the requirements of the waterway and shippers.