Plant rhizomes and roots occur in terrestrial ecosystems since at least the Devonian, but the documentation of belowground plant tissues is sparse in the fossil record. In this study, fossils representing belowground rhizomes and roots are described from the top of the Upper Yaopo Formation (Middle Jurassic), at the Yuejiapo section, Mentougou District, Beijing, China. Morphological studies of the plant fossils, together with lithofacies analyses, provide new information on plant–soil interactions during the Jurassic period. Three types of rooting systems are recognized from two fossiliferous beds. The Bed-1 Flora is interpreted as representing a Cladophlebis-dominated community, where abundant foliage remains mainly of Cladophlebis cf. scariosa and Cladophlebis delicatula are associated with Type-A rooting system. The Bed-2 Flora includes Type-B and Type-C rooting systems, although the floristic composition is unknown due to the absence of identifiable foliage remains. The Type-A and Type-B rooting systems consist of abundant in situ vertical rhizomes, fine shoot-borne roots and lateral roots, and are consistent with those of some extant ferns. The Type-C rooting system shows a thick central taproot and at least three orders of lateral roots, an architecture typical of various gymnosperms. The in situ rooting systems, as well as sedimentary evidence, contribute to the recognition of stacked, reworked Entisols in a dynamic waterlogged environment.