In recent years, liner-shipping companies have faced a traditional trade-off between cost and emission (CO2 and SOX) reduction. This study considers this element to construct a liner-shipping network design model which includes a package-cargo transport plan, route allocation, and route design. The objective is to maximize profit by selecting the ports to be visited, the sequence of port visits, the cargo flows between ports, and the number/operating speeds of vessels. In addition, emission control areas (ECAs) exist in the liner network. With reference to the idea of the column generation algorithm, this study proposed a heuristic algorithm based on empirical data through a real case calculation and selected the optimal scheme, which is in-line with both economic and environmental benefits. The results show that the model and optimization method are feasible and provide an effective solution for the liner network design of shipping companies, while also considering environmental factors. In addition, the effects of the number of ECAs, inter-port origin-destination (OD) demand, freight rate, fuel price, and carbon prices on the design of transport networks are discussed to provide a reference for the operation of shipping companies and government decision-making.