Limited knowledge about the evolution of Pacific deepwater circulation during the early-mid Miocene hinders us from understanding the relationship between global climate and deepwater circulation during this interval. The marine pelagic brown/green sediments that formed in relation to deep ocean ventilation has crucial implications for the evolution of deepwater circulation. Here, we present sedimentological, mineralogical and geochemical records (reflectance a*, grain size, clay minerals, major and trace elements, and Sr-Nd isotopes) from brown and green claystone (∼19–12 Ma) from the South China Sea (SCS) International Ocean Discovery Program (IODP) Site U1503A to study the unique conditions that caused the sediment color transition and to reveal their implications for paleoclimate and paleoceanography. The results show that the sediment color transition was dictated by the variation in Fe (III) oxides (hematite). Clay minerals, rare earth elements and Sr-Nd isotope records reveal relatively stable provenances (mainly South China and Luzon). The poor correlation between sediment color and weathering proxies (endmember 3 (eolian dust), chemical index of alteration, Ti/Na, Al/K, and smectite/(illite + chlorite)) indicates that the influence of weathering intensity changes on sediment color may be negligible. The less enriched redox-sensitive elements (Ni, Co, V, Cr, and U) in brown claystone suggest a more oxidizing sedimentary environment than that of green claystone. We attribute this difference in redox conditions to the variations in the oxygen-rich bottom current in the northern SCS, which could reflect the changes in Pacific deepwater circulation. The synchronous variations in sediment color and global benthic isotope oxygen stack imply that Pacific deepwater circulation reorganized during the early-mid Miocene warmer-colder periods.