The timing of marine ecosystem recovery following the End Permian Mass Extinction (EPME) remains poorly constrained given the lack of radiometric ages. Here we develop a high-resolution carbonate carbon isotope (δ(13)Ccarb) record for 3.20 million years of the Olenekian in South China that defines the astronomical time-scale for the critical interval of major evolutionary and oceanic events in the Spathian. δ(13)Ccarb documents eccentricity modulation of carbon cycling through the period and a strong obliquity signal. A shift in phasing between short and long eccentricity modulation, and amplification of obliquity, is nearly coincident with a 2% decrease in seawater δ(13)CDIC, the last of a longer-term stepped decrease through the Spathian. The mid-Spathian shift in seawater δ(13)CDIC to typical thermocline values is interpreted to record a major oceanic reorganization with global climate amelioration. Coincidence of the phasing shift with the first occurrence of marine reptiles (248.81 Ma), suggests that their invasion into the sea and the onset of a complex ecosystem were facilitated by restoration of deep ocean ventilation linked mechanistically to a change in the response of the oceanic carbon reservoir to astronomical forcing. Together these records place the first constraints on the duration of the post-extinction recovery to 3.35 myr.