Human activities currently play a dominant role in shaping and eroding Earth’s biodiversity, but the historical dynamics leading to this situation are poorly understood and contentious. Importantly, these dynamics are often studied and discussed without an emphasis on cultural evolution, despite its potential importance for past and present biodiversity dynamics. Here, we investigate whether cultural filtering, defined as the impact of cultural evolution on species presence, has driven the range dynamics of five historically widespread megafauna taxa (Asiatic elephant, rhinoceroses, tiger, Asiatic black bear, and brown bear) across China over the past 2 millennia. Data on megafauna and sociocultural history were compiled from Chinese administrative records. While faunal dynamics in China are often linked to climate change at these time scales, our results reveal cultural filtering as the dominant driver of range contractions in all five taxa. This finding suggests that the millennia-long spread of agricultural land and agricultural intensification, often accompanied by expansion of the Han culture, has been responsible for the extirpation of these megafauna species from much of China. Our results suggest that cultural filtering is important for understanding society’s role in the assembly of contemporary communities from historical regional species pools. Our study provides direct evidence that cultural evolution since ancient times has overshadowed climate change in shaping broadscale megafauna biodiversity patterns, reflecting the strong and increasing importance of sociocultural processes in the biosphere.