The inner Qinling Mountain basin is an ideal geographic area for examining the adaptation of the Yellow River Civilization into the transition zone of subtropical and warm temperate climates. Paleosol isotope and other geochemical and geophysical analyses were used to examine ancient farming and animal raising strategies, food structure, and past environment at the Zijing site on the inner Qinling Mountain basin. The organic carbon isotope suggests that the Neolithic and Bronze Age farmers in Zijing could cultivate up to 50% millet-like C-4 plants, developed from the Yellow River Civilization, and 50% C-3-like local plants during the interval from the Yangshao to the Xia-Shang cultures. The carbonate carbon isotope suggests that Zijing farmers could raise livestock on a relatively large scale during the Yangshao and Longshan periods. The carbon isotopic results are in agreement with other geochemical parameters, including soil organic and carbonate carbon contents, as well as the ratio of organic carbon and nitrogen. Magnetic susceptibility indicates a warmer and wetter climate condition from the Yangshao to the Xia-Shang cultures that facilitated agricultural development at this Neolithic site. The long cultural sequence sampled at this site shows that the millet-based agricultural system of the Yellow River Civilization at the Zijing site on the inner Qinling Mountain basin could have been practiced. In addition, the unusually negative delta C-13(sc) values likely also reflected a highly developed ancient agricultural civilization, which potentially has important implications for archaeology in China because of the southernmost record of millet agriculture in the Zijing site.