In order to promote the two-way flow of “urban industrial products to the countryside” and “rural agricultural products to the city”, based on the investigation and analysis of the operation characteristics of the logistics network of county-township-village under the urban-rural distribution system, a new variety of two-echelon vehicle routing problem is investigated by considering multi-commodity and simultaneous pickup and delivery. A mixed integer programming model with the optimization objective of minimizing the traveling route cost and fixed dispatching cost is established, some valid inequalities are derived to improve the performance of the model, a high-efficiency heuristic is designed to solve large-scale problems. Using the county-village-village logistics data of Jiaozuo city and Hebi city in Henan province to simulate and generate 27 different sized instances to verify the effectiveness and solving performance of the model, valid inequalities and heuristic algorithm. The experimental results show that: 1) The model established is effective, and the optimal solution can be obtained for small-sized instances within 1 hour. 2) The valid inequalities proposed can help the model obtain more optimal solutions or high-quality upper and lower bounds. 3) The heuristic algorithm proposed can quickly obtain near optimal solutions for small sized instances and satisfactory solutions for large sized instances. 4) With the increase of the size of the instances (the number of township logistics centers, the number of village logistics centers, and the number of commodity types), the difficulty of solving the problem increases sharply. 5) If the loading capacity of large/small trucks is expanded by 50% respectively, the transportation cost will be significantly reduced. Thus, the logistics cost can be effectively reduced by optimizing the loading decisions and travel route decisions through reasonable configuration of models. This research will not only expand the existing theory of two-echelon vehicle routing problem, but also provide decision support for urban and rural logistics decision-making, and then help the rural revitalization strategy.