A quantitative investigation of the ecological changes of shallow-marine benthos was undertaken at the Permian–Triassic boundary section at Zhongzhai, South China. The studied fossil material primarily included brachiopods and bivalves owing to their abundance throughout the section, but other subordinate taxonomic groups including ostracods and microgastropods were also integrated for discussion. Overall, a succession of three benthonic paleocommunities was recognized representing three connected ecological evolutionary stages across the Permian–Triassic transition. Both Stage 1 and Stage 2 paleocommunities predated the end-Permian boundary mass extinction, and were characterized by relatively high diversity of brachiopods and bivalves, with no or very rare other taxa. Approaching the end-Permian mass extinction and the PTB itself, the paleocommunity abruptly changed and was replaced by the Stage 2 paleocommunity that was characterized by a relatively low Shannon's diversity (H) coupled with a high Simpson's dominance index (D) and, most notably, a changeover from Neochonetes to Tethyochonetes (both are brachiopod genera) as the most significant ecological dominants. This Simpson's dominance index (D) shift correlates well with food shortage (i.e. much reduced terrestrial influx and acritarch abundance), and is therefore interpreted to signify, possibly, intensified interspecific competitions with Tethyochonetes seemingly outcompeting Neochonetes presumably due to its preadapted smaller body size. The post-extinction (Stage 3) paleocommunity is distinguished by a highly characteristic low-diversity and high-abundance fauna comprised mainly of lingulid brachiopods, Claraia bivalves, microgastropods and ostracods, suggesting a unique and highly stressful ecological regime. In this paleocommunity, Claraia might have acted like a “disaster taxon” and, as such, its ecological functional role in the paleocommunity was activated and elevated because of exceptional ecological conditions (e.g., anoxia, hyperthermal and/or severe food shortage). From the studied section, a number of ecological traits including species abundance distribution, Shannon's diversity (H), community dominance and body-size structure were identified as demonstrating significant changes accompanying community replacement prior to the end-Permian mass extinction. The fact that these changes preceded the mass extinction may suggest that these traits could represent some early warning signals for an impending ecological regime shift. This extended interpretation clearly has significant implications for modern ecological studies to predict future impending ecological regime shifts.