In order to explore the positive impact of the joint distribution model on the reduction in logistics costs in small-scale logistics enterprises, considering the demand on enterprises for simultaneous pick-up and delivery, as well as the cost of carbon emissions, this study considers the vehicle routing problem of simultaneous pick-up and delivery under a joint distribution model. First of all, an independent distribution model and a joint distribution model including fixed transportation, variable transportation, time penalty, and carbon emissions costs are established; second, by adding the self-adaption cross-mutation probability and the destruction and repair mechanism in the large-scale neighborhood search algorithm, the genetic algorithm is improved to adapt to the solution of the model in this paper, and the effectiveness of the improved algorithm is verified and analyzed. It is found that the improved genetic algorithm is more advantageous than the original algorithm for solving the problems of both models designed in this paper. Finally, the improved genetic algorithm is used to solve the two models, and the results are compared and analyzed. It is found that the joint distribution model can reduce the total cost by 6.61% and the carbon emissions cost by 5.73%. Additionally, the impact of the carbon trading mechanism on the simultaneous pick-up and delivery vehicle routing problem under the joint distribution model is further explored. The results of this study prove that enterprises can effectively reduce costs, improve profits, reduce carbon emissions, and promote the sustainable development of logistics enterprises under the condition of joint distribution.