Pickup and delivery problem is commonly exist in logistics system, and its optimization considering time windows is essential in practical application. Meanwhile, with the increasing awareness of environmental protection, carbon emissions should also be considered during the routing design. In this paper, a low-carbon model is introduced for the pickup and delivery problem with time windows; a division method is proposed for the different delivery costs of logistics customers in different regions; a capacity constraint processing approach is proposed to solve the capacity of the vehicle during driving. Since the requirements for the logistic system are described by several objective formulations, the multi-objective approach is adopted to solve the optimization problem. The experiment selects two sets of Shanghai logistics data at different scales. Feasible solutions with advantages of different expectations can be obtained from the experiment result.