Archaeobotanical research at the Yuezhuang and Xihe sites of the Houli culture in the Lower Yellow River has found abundant carbonised plant remains, including rice, millet, weed seeds and many other plants (7800-7000 cal BP). Although studies of the diverse economic practices of the Houli people have begun, issues such as ecological diversity and relationships between site formation processes with environmental changes are still poorly understood. Applying soil micromorphology and related methods such as particle size distribution and loss-on-ignition at Yuezhuang, this paper presents results of the geoarchaeological investigation and the implications for the reconstruction of site formation processes in relation to river alluvial history. A long alluvial sequence is reconstructed, consisting of frequent alternations of short-periods surface stabilities and succeeding alluviations. Human occupations corresponded to those short-term surface stabilities and are evidenced by the presence of anthropogenic inclusions in thin sections, including burned bone fragments and pottery sherds. The significances of this study to an ecological approach focusing on environmental changes and cultural adaption are discussed.