The habitability and ecology of Earth is fundamentally shaped by surface temperature, but the temperature history of our planet is not easily reconstructed before the evolution of early biomineralizing animals. This work presents a billion year, high-resolution, mineral-specific record of oxygen isotope measurements in shallow marine rocks. Clumped-isotope paleothermometry results from four minerals resolves previous ambiguity with seawater oxygen isotope composition and confirms that long-term cooling punctuated by higher-frequency variations are dominant components of this record. We consider post-depositional effects by comparing Phanerozoic rock and fossil records, and identify temporal and spatial controls on alteration. Key differences in the dolomite oxygen isotope record exist between the Neoproterozoic (1000–538.8 Ma) and the Phanerozoic (538.8–0 Ma), suggesting a shift from proto-dolomite or primary dolomite to secondary dolomite formation processes. This record, when viewed alongside the fossil record, suggests temperature change is tightly coupled to extinction and origination in the history of life and carbon cycle perturbations over the last billion years.