In order to clarify the impact of carbon emission limit and carbon tax rate on the path selection of refrigerated container multimodal transport, a dual objective path selection model with the lowest total transportation cost and carbon emission was constructed based on the constraints of transportation time and considering the impact of factors such as transportation speed and deadweight tonnage on carbon emission. A hybrid algorithm of genetic algorithm and simulated annealing was designed to solve the problem, and the scenario was discussed by using a study simulation. The results show that for refrigerated container transportation, increasing the transportation speed will increase the carbon emission and reduce the total transportation cost, and the increase of vehicle tonnage can reduce the unit carbon emission in transportation; changing the carbon emission limit and carbon tax rate can reduce carbon emissions in transportation and guide multimodal transport decision-makers to choose low-carbon transportation routes. The model can provide a theoretical basis for multimodal transport operators to make green path decisions.