We studied the mid-Holocene climate change in eastern Qinghai Province, China and its impact on the evolution of Majiayao (3980–2050 BC) and Qijia (2183–1635 BC) cultures, near the important Neolithic site of Changning. The investigation focused on analyses of grain size, magnetic susceptibility, ratios of elemental contents, and pollen assemblage from a loess-paleosol sequence. The results indicate that the climate was wet during 5830–4900 cal yr BP, which promoted the development of early-mid Majiayao culture in eastern Qinghai Province. However, 4900–4700 cal yr BP were drought years in the region, responsible for the decline and eastward movement of prehistoric culture during the period of transition from early-mid to late Majiayao culture. The climate turned wet again during 4700–3940 cal yr BP, which accelerated the spread of Qijia culture to the middle reaches of the Huangshui River, including the Changning site.