Early Eocene hyperthermals are geologically short-lived global warming events and represent fundamental per-turbations to the global carbon cycle and the Earth's ecosystem due to massive additions of isotopically light carbon to the ocean-atmosphere system. They serve as ancient analogs for understanding how the oceanic car-bonate system and surface-ocean ecosystem would respond to ongoing and future climate change. Here, we present a continuous carbonate record across the Eocene Thermal Maximum 2 (ETM2 or H1, ca. 54.1 Ma) and H2 (ca. 54 Ma) events from an expanded section at Ocean Drilling Program Site 1258 in tropical Atlantic. The abundant calcareous nannofossils and moderate carbonate content throughout the studied interval suggest this record was deposited above the calcite compensation depth (CCD), but below the lysocline and under the in-fluence of terrestrial dilution. An Earth system model cGENIE is used to simulate the carbon cycle dynamics across the ETM2 and H2 to offer insights on the mechanism of the rapid warming and subsequent recovery in climate and ecosystem. The model suggests moderate changes in ocean pH (0.1–0.2 unit) for the two scenarios, biogenic methane from a rechargeable methane capacitor and organic matter oxidation from thawing of the permafrost. These pH changes are consistent with a recent independent pH estimate across the ETM2 using boron isotopes. The carbon emission flux during the ETM2 is at least an order of magnitude smaller than that during the Pale-ocene–Eocene Thermal Maximum (PETM) (0.015–0.05 Pg C yr-1 vs. 0.3–1.7 Pg C yr-1). The comparable pre-and post-event carbonate contents suggest the lysocline did not over deepen following the ETM2 at this tropical Atlantic site, indicating spatial heterogeneity in the carbonate system due to strong dilution influence from terrestrial weathering and riverine discharge at Site 1258.