The Permian–Triassic mass extinction is characterized by a massive injection of carbon dioxide associated with Siberian Traps volcanism, pronounced global warming and ocean acidification. However, in the absence of high-resolution records of atmospheric CO₂ (\(p_{{\mathrm{CO}}_2}\)), detailed changes in the carbon cycle and their relationship to biosphere perturbations remain unresolved. Here we present a continuous and high-resolution \(p_{{\mathrm{CO}}_2}\) record and quantitative estimates of marine phytoplankton community structure across this interval, using carbon and nitrogen isotope analyses of chlorophyll degradation products from the Shangsi section, China. We find that the first extinction pulse in the latest Permian coincided with a minimum in \(p_{{\mathrm{CO}}_2}\), which was followed by a rapid rise to a prolonged high \(p_{{\mathrm{CO}}_2}\) interval that persisted through the second extinction pulse in the Early Triassic, and that cyanobacteria increasingly dominated marine export production between these two pulses. While the first extinction appears to have been associated with intense initial weathering that briefly suppressed the \(p_{{\mathrm{CO}}_2}\) rise and promoted eutrophy and anoxia-driven habitat loss, incorporating our observations into a biogeochemical model indicates the second extinction was sustained by reduced export production driven by the expansion of bacterial production in response to oligotrophic conditions. Such conditions were potentially caused by a long-term failure of the weathering feedback and may mark a catastrophic combination of food web collapse, hyperthermal climate and hypercapnia.