In view of the problems such as long departure interval, low occupancy rate, low profit, high cost of rural express delivery and poor delivery time that the development of urban and rural public transport in China faced, the paper put forward a solution to the urban and rural public transport operation and dispatching considering small-scale express. Firstly, the operation mode of “urban and rural public transport + small express” was put forward based on the analysis of rural small-scale express transportation demand and urban-rural public transport supply, and its influential factors were analyzed. Secondly, game theory and multi-objective programming theory were used to construct a double-objective scheduling optimization model which maximizes the income of public transport companies and minimizes the shortest travel time of passengers, considering the benefits of the new urban-rural public transport companies, passengers and small-scale express enterprises. And genetic simulated annealing algorithm was designed to provide a solution for the model. Finally, Huazhou District of Weinan City in Shaanxi Province was taken as an example to verify the solution. The comparative analysis between optimization and actual operation results shows that the scheduling optimization model constructed under the new mode has good optimization effect. It verifies the feasibility of the new model and the effectiveness of the model.