Rural areas have experienced depopulation, leading to low transport demand. Areas with low demand pose numerous challenges for conventional public transport, often characterized by limited service hours and poor accessibility, which increases reliance on private cars among rural residents. Furthermore, rural regions typically demonstrate low efficiency in logistics services, with operators facing high operating costs due to underutilization of vehicle capacities. To address these challenges, on-demand integrated passenger-freight services have been suggested as more flexible and efficient solutions for both passenger and freight transport in rural areas. This paper aims to provide a methodological framework for designing these services by utilizing mobile phone big data to identify the study area and desire lines, developing a Stated Preference survey, and proposing simulation tools to assess performance and fleet size. This methodological framework is crucial for policymakers, logistics providers, and transit operators intending to implement on-demand integrated passenger-freight services in rural areas.