The lower reaches of the Wujiang River, with complex topography and diverse environment, are located in southeast Chongqing City, where is typical research areas for exploring strategy of human adaptation to multifarious local conditions in southwest China. Structure of agriculture production experienced significant dynamics in Chongqing during the Song Dynasty (AD 960-1279) and it was regarded as golden time period of agriculture development. In present study, agricultural economy of the new excavated Caiba ((sic)(sic) in Chinese) site, as a representative site in the Wujiang River in the Song Dynasty, was reconstructed by employing biological proxies including macro seeds, palynology, and micro charcoals. Results show that agricultural activities of the Caiba site were distinctly intensified, which were specifically manifested by that inhabitants cultivated as much as ten species of cereal crops, and they not only sufficiently used flat and narrow river terraces with limited farmland resources to develop small-scale rice paddy farming, but also adequately extended farming space upwards to widely distributed and arid hillside fields with gentle slope for cultivating foxtail millet in a large scale. The sophisticated multimodal agriculture dominated by dryland farming in the Caiba site was inconsistent with that of other contemporary sites in Chongqing. We suggest that these crops with different degrees of importance clearly reveal flexible adaptation strategy featured by that inhabitants adjusted to agricultural production structure according to heterogeneous local survival niche under complex mountainous hilly landforms and virous hydrological climate conditions.