China rivers are abundant in water resources, and inland container transport is the main form of river transport. However, with the rapid development of road construction, the continuous improvement of the comprehensive transport system and increased competition in road transportation resulting in lower freight costs, inland container transport will also face huge challenges. In order to utilise the economical and energy-saving role of inland river transport more effectively, it is necessary to encourage owners of goods to choose the waterway transportation mode. From the perspective of the inland container transport system, this paper conducts a quantitative analysis to address the issue of modal choice between inland container transport and road transport, internalising the economic externality of carbon emission through the total cost of transport. Taking into account the low-carbon objective, a transportation mode choice equilibrium model based on an inland container transport system was constructed. Meanwhile, the paper focuses on analysing the economic characteristics of total transportation costs and related influencing factors using an economic approach. Finally, the model's validity is verified using numerical examples. The results demonstrate that, under the low-carbon objective, it is more economical for owners to choose waterway transportation when the transportation distance is more than 1 100 km.