To achieve the low-carbon and efficient transportation service, focusing on integrating the urban short-distance transport systems for the passenger and freight, a point-routing problem taking subway as the backbone networks of urban distribution is proposed. From the perspective of minimizing delivery time of goods, the selection decisions of distribution centers, subway exit stations and after-exit distribution routes are optimized systematically. Then an improved recursive granular algorithm is designed for solving the problem. The practicality and effectivity of the model and algorithm are tested taking the Chengdu subway as a case. The result shows that the urban distribution system based on subway can ensure the freight delivering to customers precisely and promptly. Also the system has the high stability, since the delivery time of freight will not increase significantly with the expansion of the service range.