In China, upper-level healthcare (ULHC) and lower-level healthcare (LLHC) provide different public medical and health services. Only when these two levels of healthcare resources are distributed equally and synergistically can the public’s demands for healthcare be met fairly. Despite a number of previous studies having analysed the spatial distribution of healthcare and its determinants, few have evaluated the differences in spatial equity between ULHC and LLHC and investigated their institutional, geographical and socioeconomic influences and spillover effects. This study aims to bridge this gap by analysing panel data on the two levels of healthcare resources in 31 Chinese provinces covering the period 2003–2015 using Moran’s I models and dynamic spatial Durbin panel models (DSDMs). The results indicate that, over the study period, although both levels of healthcare resources improved considerably in all regions, spatial disparities were large. The spatio-temporal characteristics of ULHC and LLHC differed, although both levels were relatively low to the north-west of the Hu Huanyong Line. DSDM analysis revealed direct and indirect effects at both short-and long-term scales for both levels of healthcare resources. Meanwhile, the influencing factors had different impacts on the different levels of healthcare resources. In general, long-term effects were greater for ULHC and short-term effects were greater for LLHC. The spillover effects of ULHC were more significant than those of LLHC. More specifically, industrial structure, traffic accessibility, government expenditure and family healthcare expenditure were the main determinants of ULHC, while industrial structure, urbanisation, topography, traffic accessibility, government expenditure and family healthcare expenditure were the main determinants of LLHC. These findings have important implications for policymakers seeking to optimize the availability of the two levels of healthcare resources.