When the current port city is developing, they are facing some universal problems to the urban traffic and environment caused by port and road transportation, of which the main part is truck transportation. Hence, a new sustainable transportation mode, i.e. underground logistic system, is proposed for the container port area. Based on the layout of the underground logistics system from Shanghai Waigaoqiao to Jiading Line and the forecasted traffic volume of the port area in Waigaoqiao Port Area, a comprehensive transport network optimization model is established from the perspectives of carbon trading, time and cost; and the rationality of implementing the underground logistics system in the port areas is analyzed further. And then the distribution of the comprehensive transport network volume is obtained by using Lingo12 solution; the conclusion that the underground logistics can reduce the cost, save the energy and reduce the emission and ease the traffic congestion is obtained. Finally, a reasonable range for carbon trading prices and unit price of underground logistics system is discussed. The experimental results can provide reference for the cargo distribution plan after the completion of the underground logistics system and the realization of the comprehensive transport network.