Abstract: The mass magnetic susceptibility and multiple elements in the early cultural strata (640~1250 cm, covering three cultural phases: late Neolithic period, Xia and Shang dynasties) in the Zhongba Site in Chongqing were tested, and the measured major elements in the late Neolithic and Xia-Shang cultural strata were classified into three types by element content median comparison and principal component analysis (PCA): (1) enriched elements: Ba, C, Cu, Ca, Mg, Mn, P, Sr; (2) depleted elements: Al, Cr, Fe, K, Na, V; and (3) slightly-changed elements: Co, Hg, Ni, Pb, Ti, Se. Based on the patterns of human activities corresponding to the characteristics of enriched or depleted elements, the variation characteristics of human activities in the three cultural phases were discussed. The lower Neolithic layer (950~1250 cm) presents increment in contents of Cu, Ba, Mg and Mn, and the accelerated losses of Cr, V, Al and K, indicating the intensification of human activities. The upper Neolithic layer (835~950 cm) shows a gradual decrease of Cu, Ba and Sr, and obvious increase of Hg, Mg and Mn, indicating that the Zhongba Site had changed from waste dumping to residential living in function. The Xia Dynasty (740~835 cm) and Shang Dynasty (640~740 cm) culture layers contain increasingly accumulated burnt-clay particles and ceramic sherds, and pose an overall increase in magnetic susceptibility and a continuous decrease in the content of depleted elements, reflecting the continuous increase in the intensity of human activities. We suggested that the changes in the contents of enriched elements, depleted elements, and other elements of Co, Fe, Mg, and Mn in the Zhongba Site are not only the result of human interference, but also the result of the combined effects of climate change and geo-biological cycles in specifically the context of rapid rainfall changes.