The largest mass extinction of biota in the Earth's history occurred during the Permian–Triassic transition and included two extinctions, one each at the latest Permian (first phase) and earliest Triassic (second phase). High seawater temperature in the surface water accompanied by euxinic deep-intermediate water, intrusion of the euxinic water to the surface water, a decrease in pH, and hypercapnia have been proposed as direct causes of the marine crisis. For the first-phase extinction, we here add a causal mechanism beginning from massive soil and rock erosion and leading to algal blooms, release of toxic components, asphyxiation, and oxygen-depleted nearshore bottom water that created environmental stress for nearshore marine animals. For the second-phase extinction, we show that a soil and rock erosion/algal bloom event did not occur, but culmination of anoxia–euxinia in intermediate waters did occur, spanning the second-phase extinction. We investigated sedimentary organic molecules, and the results indicated a peak of a massive soil erosion proxy followed by peaks of marine productivity proxy. Anoxic proxies of surface sediments and water occurred in the shallow nearshore sea at the eastern and western margins of the Paleotethys at the first-phase extinction horizon, but not at the second-phase extinction horizon. Our reconstruction of ocean redox structure at low latitudes indicates that a gradual increase in temperature spanning the two extinctions could have induced a gradual change from a well-mixed oxic to a stratified euxinic ocean beginning immediately prior to the first-phase extinction, followed by culmination of anoxia in nearshore surface waters and of anoxia and euxinia in the shallow-intermediate waters at the second-phase extinction over a period of approximately one million years or more. Enhanced global warming, ocean acidification, and hypercapnia could have caused the second-phase extinction approximately 60 kyr after the first-phase extinction. The causes of the first-phase extinction were not only those environmental stresses but also environmental stresses caused by the soil and rock erosion/algal bloom event.