Massive carbon dioxide (CO2) emissions are widely assumed to be the driver of the end-Permian mass extinction (EPME). However, the rate of and total CO2 released, and whether the source changes with time, remain poorly understood, leaving a key question surrounding the trigger for the EPME unanswered. Here, we assimilate reconstructions of atmospheric PCO2 and carbonate δ13C in an Earth system model to unravel the history of carbon emissions and sources across the EPME. We infer a transition from a CO2 source with a thermogenic carbon isotopic signature associated with a slower emission rate to a heavier, more mantle-dominated volcanic source with an increased rate of emissions. This implies that the CO2 degassing style changed as the Siberian Traps emplacement evolved, which is consistent with geochemical proxy records. Carbon cycle feedbacks from terrestrial ecosystem disturbances may have further amplified the warming and the severity of marine extinctions.