To facilitate residents travel along inter-city expressway, the setting method of passenger sites on inter-city expressway was proposed. In accordance with the operating features of passenger lines on inter-city expressway, an algorithm was proposed to achieve full coverage for all settlements by seeking the minimum number of settlement sets. Optimization model was established with the target of minimizing total walking distance to determine the best place of each passenger site corresponding with settlement set. In order to improve the operational efficiency of passenger lines, grey clustering method was introduced and the quantitative clustering index system was established to optimize the number of sites by assessing the important degree of each site. Finally, the above method was validated by a case study. The results show that it is an effective approach for setting sites. The method achieves dual optimization for the location and the number of passenger site, meets the demand of the most residents along the intercity expressway, and makes site layout more reasonable on inter-city expressway.