Surface energy balance and the partitioning of sensible heat flux (SHF) and latent heat flux (LHF) play key roles in land–atmosphere feedback. However, the lack of long-term observations of surface energy fluxes, not to mention spatially extensive ones, limits our understanding of how the surface energy distribution has responded to a warming climate over recent decades (1979–2009) at the national scale in China. Using four state-of-the-art reanalysis products with long-term surface energy outputs, we identified robust changes in surface energy partitioning, defined by the Bowen ratio (BR = SHF/LHF), over different climate regimes in China. Over the past three decades, the net radiation showed an increasing trend over almost the whole of China. The increase in available radiative energy flux, however, was balanced by differential partitioning of surface turbulent fluxes, determined by local hydrological conditions. In semi-arid areas, such as Northeast China, the radiative energy was transferred largely into SHF. A severe deficiency in near-surface and soil moistures led to a significant decreasing trend in LHF. The combined effect of increased SHF and decreased LHF resulted in significant upward trends in the BR and surface warming over Northeast China. In contrast, in the wet monsoon regions, such as southern China, increased downward net radiation favored a rise in LHF rather than in SHF, leading to a significant decreasing trend in the BR. Meanwhile, the increased LHF partly cancelled out the surface warming. The warming trend in southern China was smaller than that in Northeast China. In addition to impacts on heat-related events, the changes in the BR also reflected recent cases of extreme drought in China. Our results indicate that information regarding the BR may be valuable for drought monitoring, especially in regions prone to such conditions.