Extinctions of large mammals characterize the Late Quaternary, spanning from the Late Pleistocene to the Anthropocene. As their causes, apart from climate change, researchers have proposed anthropogenic factors with focus on roles of early foraging behaviors (e.g. hunting and using fire) and industrial development in mammal range contractions and final extinctions. However, much less is known about how such events have unfolded in agricultural societies that lie evolutionarily between Paleolithic ones and modern ones. To fill the gap, using spatiotemporal data derived from historical records in ancient China over the past two millennia, we analyzed the patterns of mammal range contractions and their associations with historical climate change and agricultural population dynamics. We found that it was the long-term upslope spread of agricultural population that consistently contracted the mammal distributions in China during the study period, while periodic warming and cooling may have contributed to temporary range fluctuations. Our study provides direct evidence that biotic interactions can overshadow climate in terms of driving species distributions even at large spatiotemporal scales and suggests that humans may have long been reshaping species distributions and the biosphere progressively in times of agriculture. Better understanding of the processes that have led to current species distribution patterns has great implications for future conservation strategies in the Anthropocene.