The emergence and enduring diffusion of COVID-19 has had a dramatic impact on cities worldwide. The scientific aim of this study was to introduce geospatial thinking to research related to infectious diseases, while the practical aim was to explore the impact on population movements and urban linkages in the longer term following a pandemic outbreak. Therefore, this study took 366 cities in China as the research subjects while exploring the relationship between urban contact and the outbreak of the pandemic from both national and regional perspectives using social network analysis (SNA), Pearson correlation analysis and multi-scale geographically weighted regression (MGWR) modeling. The results revealed that the number of COVID-19 infections in China fluctuated with strain variation over the study period; the urban contact network exhibited a significant trend of recovery. The pandemic had a hindering effect on national urban contact, and this effect weakened progressively. Meanwhile, the effect exhibited significant spatial heterogeneity, with a weakening effect in the eastern region ≈ northeast region > central region > western region, indicating a decreasing phenomenon from coastal to inland areas. Moreover, the four major economic regions in China featured border barrier effects, whereby urban contact networks constituted by cross-regional flows were more sensitive to the development of the pandemic. The geostatistical approach adopted in this study related to infectious disease and urban linkages can be used in other regions, and its findings provide a reference for China and other countries around the world to respond to major public health events.