Against the backdrop of new urbanization and urban-rural integration, research on rural resident mobility patterns in megacity fringe areas provides insights into addressing challenges in urban-rural spatial governance. Using mobile phone signaling data and a geographically weighted regression (GWR) model, this paper examines the spatiotemporal characteristics of rural resident mobility across multiple scales and the underlying mechanisms in Tongzhou District, Beijing. The results show that: ① Village-to-village mobility sustains the basic rural resident mobility network, while village-to-district central area flows significantly exceed village-to-town/township central area flows. On weekends, rural-to-urban mobility intensifies and extends to the central city and surrounding suburban districts, generating new urban-rural interaction patterns. ② In the inner suburbs, mobility intensity follows a dual-core–periphery gradient pattern centered on the Beijing Municipal Administrative Center and Yizhuang New Town, whereas the outer suburbs exhibit a dispersed cluster pattern centered on key villages and town/township central areas, challenging the assumption of spatial homogeneity inherent in core–periphery theory. ③ The effects of the influencing factors demonstrate spatial heterogeneity. High-level mobility in the inner suburbs is governed by urban-rural location and transportation infrastructure, whereas localized mobility in the outer suburbs is primarily shaped by public service facilities and socio-economic conditions. Accordingly, the paper proposes differentiated planning strategies: strengthening rapid transit networks in the inner suburbs and fostering specialized industries in the outer suburbs. These strategies provide a scientific basis for promoting the flow of urban-rural production factors and enhancing spatial governance in megacity fringe areas.