The late Paleocene and early Eocene (LPEE) are characterized by long-term (million years, Myr) global warming and by transient, abrupt (kiloyears, kyr) warming events, termed hyperthermals. Although both have been attributed to greenhouse (CO2) forcing, the longer-term trend in climate was likely influenced by additional forcing factors (i.e., tectonics) and the extent to which warming was driven by atmospheric CO2 remains unclear. Here, we use a suite of new and existing observations from planktic foraminifera collected at Pacific Ocean Drilling Program Sites 1209 and 1210 and inversion of a multiproxy Bayesian hierarchical model to quantify sea surface temperature (SST) and atmospheric CO2 over a 6-Myr interval. Our reconstructions span the initiation of long-term LPEE warming (~58 Ma), and the two largest Paleogene hyperthermals, the Paleocene-Eocene Thermal Maximum (PETM, ~56 Ma) and Eocene Thermal Maximum 2 (ETM-2, ~54 Ma). Our results show strong coupling between CO2 and temperature over the long- (LPEE) and short-term (PETM and ETM-2) but differing Pacific climate sensitivities over the two timescales. Combined CO2 and carbon isotope trends imply the carbon source driving CO2 increase was likely methanogenic, organic, or mixed for the PETM and organic for ETM-2, whereas a source with higher δ13C values (e.g., volcanic degassing) is associated with the long-term LPEE. Reconstructed emissions for the PETM (5,800 Gt C) and ETM-2 (3,800 Gt C) are comparable in mass to future emission scenarios, reinforcing the value of these events as analogs of anthropogenic change.