Extreme climatic events have profound impacts on human society. Here we present the results of a study of organic biomarkers within a sedimentary section at the archaeological site of Yuchisi, eastern China, in order to reconstruct climatic variability during the Dawenkou (5,050-4,400 yr BP) and Longshan (4,400-4,000 yr BP) cultures. At ~4,400 yr BP, within the cultural transition horizon, abrupt changes in biomarkers, such as the fatty acid ratio C18:2/C18:0, 2C31/(C27 + C29), n-C18-ol and n-C30-ol, indicate the occurrence of local climate changes over the course of a few decades. These changes occurred during the transition from the Holocene warm period to a subsequent cold period which lasted for the following 600 years. This climatic shift has been recorded at numerous sites worldwide, and it is likely to have been the main cause of the widespread collapse of many isolated cultures at that time. The palaeoclimatic and archaeological data from the Yuchisi sediments may provide new insights into the relationship between climate change and prehistoric cultural transitions.