The United Nations Sustainable Development Goals (SDGs) and the rise of global sustainability science have led to the increasing recognition of basins as the key natural geographical units for human–land system coupling and spatial coordinated development. The effective measurement of spatiotemporal patterns of urban connectivity within a basin has become a key issue in achieving basin-related SDGs. Meanwhile, China has been actively working toward co-ordinated regional development through in-depth implementation of the Yellow River Basin’s ecological protection and high-quality development. Urban connectivity has been trending in urban planning, and significant progress has been made on different scales according to the flow space theory. Nevertheless, few studies have been conducted on the multiscale spatiotemporal patterns of urban agglomeration connectivity. In this study, the urban network in the Yellow River Basin was constructed using Tencent population migration data from 2015 and 2019. It was then divided into seven distinct communities to enable analysis at both the basin and community scales. Centrality, symmetry, and polycentricity indices were employed, and the multiscale spatiotemporal patterns of urban agglomerations in the Yellow River Basin were identified using community detection, complex networks, and the migration kaleidoscope method. Community connectivity was notably concentrated at the basin scale with a centripetal pattern and spatial heterogeneity. Additionally, there was a symmetrical and co-ordinated relationship in population migration between the eastern and western regions of the basin, as well as between the internal and external parts of the basin. At the community scale, there was significant variation in the extent of central agglomeration among different communities, with few instances of similar-level, long-distance, and interregional bilateral links. The utilization of multiscale spatiotemporal patterns has the potential to enhance the comprehension of economic cooperation between various cities and urban agglomerations. This understanding can aid decision-makers in formulating sustainable development policies that foster the spatial integration of the basin.