To optimize the container multimodal transportation path selection problem with differences in cargo time sensitivity, this paper introduces the concept of mixed time windows and establishes an integer programming model from the perspective of carriers. The objective is to minimize the total transportation cost while meeting the customer’s on-time delivery requirements. The model imposes hard time window constraints on cargoes with on-time delivery requirements and soft time window constraints on general cargoes. A bi-level genetic algorithm is employed to solve the model. A case study is conducted to demonstrate the effectiveness of the proposed approach. Experimental results show that the bi-level genetic algorithm’s convergence ability, efficiency, stability, and global search capabilities are far superior to those of traditional single-level genetic algorithms. This indicates that the use of multi-stage solution approaches can mitigate the shortcomings of genetic algorithms in dealing with high-dimensional problems. In addition, when analyzing the effects of time penalty intensity and time window on decision-making results, it is found that the more time-sensitive cargoes are more likely to be affected by the time window setting, and will tend to sacrifice costs to ensure that the time demand is met. At the same time an increase in demand for time-sensitive services is accompanied by an increase in operating costs. Accurate assessment and classification of time sensitivity of cargoes can effectively prevent wasting resources in unnecessary areas, and ultimately maximize decision outcomes and ensure the most efficient use of resources.