The origin and sedimentary environment of the Late Tertiary (Neogene) Red Clay Formation in northern China had long been controversial. A new mollusk record from the Xifeng red clay (red-earth) sequence in the central Loess Plateau provides the biological evidence for addressing questions of its origin and environmental implication. The study of composition and preservation condition of seventy mollusk fossil assemblages reveals the initial ecological condition of the red clay formation, avoiding the effect of post-deposited alteration. The result shows that all of identifiable mollusk species are composed of terrestrial taxa, most of them are the common species found in the overlying Quaternary loess-paleosol sequence. Most of fossil individuals preserved in the red clay strata are in living conditions based on the investigation of fieldwork, indicating the original population. Thus, the mollusk fossil assemblages can be used as an indicator of primary environment of the red clay formation. The mollusk record from the Xifeng red clay sequence supports the view that the red clay is an aeolian origin, similar to the overlying Quaternary loess deposits. Our data also reveal the history of environmental changes at Xifeng from 6.2–2.4 Ma, which is coupled in phase with the formation and development of the Arctic ice sheets and the process of the Tibetan Plateau uplift. Both may be the major cause and forcing mechanisms of the late Tertiary environmental changes in the Loess Plateau.