To reduce the commuting costs of employees in remote areas, an employer bus alliance operation model was designed, and a two-layer optimization model was constructed for bus alliance operation. Among them, the upper level model targeted the total generalized cost of all employer buses minimum, and optimizing the member structure of participating bus alliances, the lower level model considered the time value differences among employers and employees within the alliance, with the goal of minimizing the total generalized cost of shuttle buses in the alliance, and optimizeed the travel paths of each shuttle bus during the operation of the alliance. The monetary costs of alliance operating shuttle buses was fairly shared based on Shapley value method. Taking three employers in the Meishan area of Ningbo as an example, the optimized shuttle bus operation plan shows that the three employers’ alliance is the optimal alliance structure. Compared with each employer operating commuting buses separately, the total generalized cost of operating shuttle buses by the alliance is saved by 10.24%, of which the monetary cost is saved by 26.44%, and the monetary cost shared by the three employers is reduced by 27.7%, 51% and 5.9% respectively; the employee time costs is saved by 3.75%。