The Pliocene epoch is considered the most recent analog of modern warming because CO2levels were similar to the present. To explore the carbonate minerals formed in the warmer Pliocene epoch, we studied two continuous sections of the Red Clay Formation on the Chinese Loess Plateau (CLP) by X-ray Diffraction (XRD), Fourier Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy (SEM) and Stable Isotope Mass Spectrometry. The Red Clay Formation on the CLP exhibits diagnostic FTIR absorption features of calcite and protodolomite. This allowed quantification of the two carbonate minerals by the FTIR method. Using the FTIR method we estimate the average concentration of protodolomite in Bajiazui is 3.6% whereas the Duanjiapo section is 6.0%. Protodolomite occurrence is more consistent and the concentration is higher from ∼6.5–4.2 Ma B.P. and decreases markedly from 4.2–2.6 Ma B.P. Red Clay protodolomite is depleted in bothδ13CPDB and δ18OPDB, ranging from −4.1‰ to −10.4 and from −6.7‰ to −11.6, respectively, and has a slightly higher δ18O value than the calcites. SEM observations show that Red Clay protodolomite is composed of euhedral rhombic crystals that range from 1–20 μm in diameter, grow into the soil voids and coexist with authigenic calcite and palygorskite. These observations imply that the protodolomite grew in situ and is authigenic from pedogenesis. Dolomitization in the Red Clay sequence appears to be the result of overcoming kinetic barriers. We propose that in the Red Clay a warm climate with seasonal dry conditions leads to the formation of calcrete from soil pore waters thereby enriching the pore solutions with respect to Mg2+ and significantly increasing the Mg/Ca ratio bringing about the formation of protodolomite.