Floods clustered in episodes are the most prevalent natural disaster worldwide, causing substantial economic and human losses. Although these events are often linked to time-periods of extreme rainstorms and unique atmospheric circulation patterns, the river basin characteristics affected by anthropogenic land use changes could exert a strong influence. However, the way and extent of how land use changes across different time scales affect flooding periods are still unclear, especially considering the historical land use changes. This study uses the Landlab landscape evolution model, coupled with an evapotranspiration model, to investigate the forcing factors for the paleo-flooding trends in the Wei River catchment over the last 5000 years. The results indicate that the flooding period from 4400 to 4000 BP was caused by an increase of 28 % in antecedent moisture content as well as a decrease of 28 % in its spatial variability, which are primarily due to climate change, and that the contribution of land-use change is less than 5 %. The increases of about 14 % and 8 % in main channel sedimentation rate play a leading role in flood generation during the time periods from 3400 to 2800 BP and 2000–1400 BP, respectively. These two periods of increased flooding are primarily caused by the erosional effects of increasing anthropogenic land use, whose contributions range from 33 % to 64 %. Furthermore, based on our modelling results, we suggest that the downstream propagation of the main flooding locations, from the Wei River to the lower reaches of the Yellow River, can be explained by the downstream migrating sediment wave. In conclusion, our simulation results give new insights into the causes of Holocene flooding periods in the middle Yellow River from the perspective of dynamic changes in catchment characteristics, which is helpful to improve regional flood risk management under future climate change and anthropogenic activities.