The Permian–Triassic climate crisis can provide key insights into the potential impact of horizon threats to modern-day biodiversity. This crisis coincides with the same extensive environmental changes that threaten modern marine ecosystems (i.e., thermal stress, deoxygenation and ocean acidification), but the primary drivers of extinction are currently unknown. To understand which factors caused extinctions, we conducted a data analysis to quantify the relationship (anomalies, state-shifts and trends) between geochemical proxies and the fossil record at the most intensively studied locality for this event, the Meishan section, China. We found that δ18Oapatite (paleotemperature proxy) and δ114/110Cd (primary productivity proxy) best explain changes in species diversity and species composition in Meishan’s paleoequatorial setting. These findings suggest that the physiological stresses induced by ocean warming and nutrient availability played a predominant role in driving equatorial marine extinctions during the Permian–Triassic event. This research enhances our understanding of the interplay between environmental changes and extinction dynamics during a past climate crisis, presenting an outlook for extinction threats in the worst-case “Shared Socioeconomic Pathways (SSP5–8.5)” scenario.