Final recovery of marine ecosystems after the end-Permian mass extinction took several million years, partly due to inhospitable environments and three episodes of further extinction that occurred during the Early Triassic: in the late Griesbachian, near the Smithian-Spathian boundary (SSB), and in the late Spathian. The SSB crisis coincides with an episode of extreme warmth, but has been little studied. This study represents the first stratigraphic and paleoecological analysis of the SSB crisis in the Nanpanjiang Basin, south China, which is a key area for Permian–Triassic studies. A comprehensive, high-resolution stratigraphic framework comprising six conodont zones is provided. Conodonts are an extinct group of marine chordates with a feeding apparatus composed of microscopic “tooth-like” elements. They are one of the fastest-evolving fossil groups, sensitive to environment stress, and are thus an ideal organism to test ecological responses to past episodes of climatic change. Detailed size measurements of 441 conodont elements of the closely related genera Neospathodus, Triassospathodus, and Novispathodus show for the first time that this clade suffered a temporary, but significant, size reduction during the SSB crisis, followed by gradual and steady size increase during the early Spathian. Size reduction of conodonts was caused by an episode of global warming, further strengthening the link between morphological and climatic changes recorded in the fossil record.