In depopulated areas, public transportation services provided by municipalities are important for traffic-vulnerable people. Some municipalities need to scale back their services due to budget shortfalls. To tackle this social and technological problem, a transdisciplinary approach is necessary. The contribution of this paper is a methodology for considering sustainable public transportation services over uncertain long term and evaluate using it in Narita City, Japan. Narita City is a complex area where urbanization by the airport and rural farming villages coexist. To estimate the impact of various conditions under public transportation services, we use QoM index, which comprehensively quantifies the quality of an individual’s mobility and can estimate the time-series changes of public transportation in the future. The simulation results show that residents’ QoM values can be divided into two groups, with a higher percentage belonging to the lower group the more likely they are to live in rural areas or to be older, due to lower availability of transportation. In contrast, as the years passed, the average QoM in the urban area decreased, while that in the other areas increased. It means the elderly gradually clustered in the urban area as the years passed by natural population changes. Findings of our design proposal for a sustainable mobility service design in Narita City are to adopt demand-responsive transport like service to satisfy the small but uncertain future demand of traffic-vulnerable people in depopulated area at low cost.