Increased flooding caused by global warming threatens the safety of coastal and river basin dwellers, but the relationship of flooding frequency, human settlement and climate change at long time scales remains unclear. Paleolithic, Neolithic and Bronze Age cultural deposits interbedded with flood sediments were found at the Shalongka site near the north bank of the upper Yellow River, northeastern Tibetan Plateau. We reconstruct the history of overbank flooding and human occupation at the Shalongka site by application of optically stimulated luminescence and radiocarbon dating, grain size, magnetic susceptibility and color reflectance analysis of overbank sediment and paleosols. The reliability of OSL dating has been confirmed by internal checks and comparing with independent 14C ages; alluvial OSL ages have shown a systematic overestimation due to poor bleaching. Our results indicate that the Yellow River episodically overflowed and reached the Shalongka site from at least ~ 16 ka and lasting until ~ 3 ka. Soil development and reduced flooding occurred at ~ 15, ~ 8.3–5.4, and after ~ 3 ka, and prehistoric populations spread to the Shalongka site area at ~ 8.3, ~ 5.4, and ~ 3 ka. We suggest that climate change influenced the overbank flooding frequency and then affected prehistoric human occupation of the Shalongka site.