High-resolution variations in carbonate minerals from the Jiaxian Red Clay section, located at the northern limit of the present East Asian summer monsoon (EASM) on Chinese Loess Plateau were quantified using Fourier transform infrared spectroscopy. We analyzed a large quantity of sediments dated from the late Miocene to Pliocene (8.2–2.6 Ma). The carbonates in this interval show high-frequency variations alternating between leached and calcareous horizons. The low carbonate contents and high values of magnetic susceptibility and high Rb/Sr ratios were found in the leached zones, a pattern that is consistent with that observed in the overlying Quaternary loess-paleosol sequences. This pattern suggests that East Asian Monsoon (EAM) rainwater enhanced leaching and accumulation processes of carbonate minerals in the Red Clay Formation in a way similar to the loess-paleosol sequence. Seven alternating leached and calcareous zones are identified, suggesting oscillations of the EASM and East Asian winter monsoon intervals. The calcareous zones were also found to have high Zr/Rb ratio. These indications of shifts from a strong EASM to East Asian winter monsoon dominance correlate well with the cooling transition indicated by deep sea δ18O isotopes. This evidence suggests that the EAM was active during the late Miocene and Pliocene and was similar to the Quaternary monsoon. The presence of a strong EAM during the Pliocene Warm Period also raises questions about the hypothesis that past and future warm climate conditions could produce a permanent El Niño-like state.