Extreme greenhouse warming in the latest Permian played a key role in the largest animal extinction event ever recorded in Earth history. The extinction was likely triggered by volcanic eruptions that dramatically increased atmospheric CO2 levels and pushed the Earth system into a lethally hot greenhouse state with stratified, anoxic and more acidic oceans. These conditions intensified a few million years later during the middle/late Smithian Thermal Maximum (STM), and a further biodiversity loss occurred during the subsequent cooling across the Smithian-Spathian boundary (SSB). The marine carbonate factory is expected to have changed during this period, but relevant studies are still lacking. Here, we report calcium isotopic data of bulk carbonate rocks (delta Ca-44/40(carb)) from two marine carbonate sections (Jiarong and Shitouzhai) in South China, showing-0.5-0.7 parts per thousand positive shift of delta Ca-44/40(carb) coupled to a 4-6 parts per thousand positive shift of delta 13Ccarb from the middle Smithian to the early Spathian. Box modeling of the marine Ca cycle yielded two scenarios (i.e., constant and variable delta Ca-44/40(seawater)) that can produce a-0.5 parts per thousand positive shift of delta Ca-44/40(carb): (1) A local mineralogical shift in primary carbonate mineralogy at both sites from 80% aragonite to 80% calcite, or (2) a >10x increase of global carbonate burial flux. The former is consistent with a-20-50-fold rise of Ca/Mg ratios and-10-50-fold decrease of Sr/Ca ratios in the study sections, and the latter fits well with massive carbonate deposition globally during the early Spathian. Oceanic overturn and upwelling of alkaline deep waters during SSB climatic cooling is proposed as the main reason for the increase in carbonate burial flux. Thus, the SSB transition marks an important step in the recovery of the marine fauna after the end-Permian mass extinction triggered by climatic cooling, ocean ventilation, and a pronounced rise in marine carbonate deposition on continental shelves.