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Spatial-interaction networks are an important factor in geography that could help in the exploration of both human spatial-temporal behavior and the structure of urban areas. This paper analyzes changes in the spatio-temporal characteristics of the Spatial-Interaction Networks of Beijing (SINB) in three consecutive steps. To begin with, we constructed 24 sequential snapshots of spatial population interactions on the basis of points of interest (POIs) collected from Dianping.com and various taxi GPS data in Beijing. Then, we used Jensen–Shannon distance and hierarchical clustering to integrate the 24 sequential network snapshots into four clusters. Finally, we improved the weighted k-core decomposition method by combining the complex network method and weighted distance in a geographic space. The results showed: (1) There are three layers in the SINB: a core layer, a bridge layer, and a periphery layer. The number of places greatly varies, and the SINB show an obvious hierarchical structure at different periods. The core layer contains fewer places that are between the Second and Fifth Ring Road in Beijing. Moreover, spatial distribution of places in the bridge layer is always in the same location as that of the core layer, and the quantity in the bridge layer is always superior to that in the core layer. The distributions of places in the periphery layer, however, are much greater and wider than the other two layers. (2) The SINB connected compactly over time, bearing much resemblance to a small-world network. (3) Two patterns of connection, each with different connecting ratios between layers, appear on weekdays and weekends, respectively. Our research plays a vital role in understanding urban spatial heterogeneity, and helps to support decisions in urban planning and traffic management. [ABSTRACT FROM AUTHOR]