The multifunctionality and sustainability of ecosystems are strongly dependent on their ability to withstand and recover from disturbances—that is, ecosystem resilience (ER). However, the dynamics and attributes of ER remain largely unknown, especially in China, where climatic and anthropogenic pressures are high. In this study, we evaluated spatiotemporal patterns of ER in China from 2001 to 2020 using solar-induced chlorophyll fluorescence. We estimated the relative independent importance of climate change, CO2, and anthropogenic factors on changes in ER signals. The results showed that more than half of the ecosystems in the study area have experienced ER gain followed by ER loss during the past two decades. Before breakpoints (BPs), climate change explained 58.29% of the ER change associated with increasing precipitation. After BPs, 65.10% of the ER change was most affected by CO2, and drought from rising temperature further deteriorated ER loss. We highlight that relationships between changes in ER and climate are spatially heterogeneous and suggest increased negative radiative effects of CO2, associated with global warming, on ecosystem stability due to the saturated canopy photosynthesis. These findings have crucial implications for future climate change mitigation, carbon peak, and carbon neutrality targets.