In scenario studies of biodiversity and ecosystem services, the population distribution is one of the key driving forces. In this study, we developed a coupling method for narrative scenarios and spatially explicit residential and working population designs for all of Japan as a common dataset for ecosystem scenario analysis implemented by 5-year project entitled ``Predicting and Assessing Natural Capital and Ecosystem Services (PANCES)’’. Four narrative scenarios were proposed by the PANCES project using two axes as major uncertainties: the population distribution and the capital preference. The residential population and the working population in primary industries were calculated using a gravity-based allocation algorithm in a manner consistent with the storylines of the PANCES scenarios. Using the population distribution assumption by scenario, the population was overlaid with the natural capital and the supply potential of ecosystem services. The results supported to understand the gaps between natural capital and maintainability, and the potential of ecosystem services and realizability. The spatially explicit population distribution data products are expected to help design the nature conservation strategy and governance option in terms of both social system and ecological system.