The formation and evolution of phaeozems have always been an area of interest because the phaeozems play an important role in two regions dubbed as "European Bread Basket" and "Northeast China Storehouse." As the phaeozems contain a large proportion of parent materials and are sensitive to human intervention, their formation and evolution have been restricted. Due to the homogeneity of loess parent material, there has been extensive research on the formation of surface phaeozems from the loess parent material. However, phaeozems developed from key fluvial parent material have so far received little attention. Therefore, key information on the formation of phaeozems is missing. In this context, this study applies geochemical tests to determine rare earth elements and major and trace elements in the deep phaeozem layer from the Arongqi borehole in the phaeozems of Northeastern China. Further, the sporopollen fossil tests were conducted in the HT-1-4-2 borehole, and the distribution characteristics of the deep phaeozem layer were analyzed using geostatistics. The results from this study indicate that rare earth data from phaeozems in Arongqi's deep layer shows a comparatively high total concentration of rare earth elements, with a mean value of 141.45 mg.kg− 1. The chondrite normalization curve demonstrates that the distribution of light rare earth elements shows a positive slope. Further, Eu shows a trend with a slight negative anomaly, while Ce shows a trend with an evident negative anomaly. Ce > -0.1 (mean value 3.9) indicates a reducing environment with hypoxia. The distribution of rare earth elements indicates that phaeozems contain transportable parent materials with trace elements Th/U > 2 (mean value 2.88), Sr/Ba < 0.6 (mean value 0.38), 0 < Rb/Sr < 0.6 (mean value 0.26), Sr /Cu > 10 (mean value 30.98), and climate index at mean value of 0.23. The presence of trace elements indicated freshwater habitats and a dry-hot to semi-dry-hot climate. The sporopollen fossils are mainly comprised of shrubs, coniferous forests, and terrestrial herbs. The presence of Ephedra and Polygonaceae indicates that the environment was hot and arid at that time. Moreover, the presence of several ferns observed in the vertical profile indicates an intermittent warm and humid climate between droughts. Thus, it can be concluded that the deep phaeozems in Arongqi developed in the floodplains of Arun River under the dry-hot-semi-dry-hot climatic conditions.