There exists growing interest in integrating social and ecological sciences to elucidate human-nature interactions from the perspective of social-ecological systems (SES). The compelling logic in the past is that people inevitably harm nature as they use it; however, people have learned to use it while protecting or even improving it. Nowadays though there is a growing emphasis on transformability into a more desirable SES with deliberate human actions rather than adapting to the existing conditions, this theory has not been tested, due to the lack of large-scale and long-term records. The millennia-long records of humans to alter SES in China's Loess Plateau provide a unique means to test ecological theories and heuristic models. Here, we demonstrated human activities can erode ecological resilience or improve it to provide better ecoservices than the pristine. Relative resilience, calculated as a ratio of annual sediment discharge anomaly to the pristine rate, decreased from 0 at the pristine state to -1 in the 1950s due to deforestation and agricultural expansion, whereas increased to about 0.8 at the present by human intervention of environmental slow variables. Building resilience by attending slow variables rather than controlling disturbance should be the goal of adaptive ecosystem management in a SES.