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Whether body size reduction (the Lilliput Effect) occurred in the Early Triassic invertebrates remains a matter of debate. Here, we investigate the size evolution of brachiopods spanning the Late Permian through the Early to Middle Triassic based on 3316 brachiopod specimens from South China. Our results show that the maximum and median size among species decreased dramatically from the latest Permian (Changhsingian) to the earliest Triassic (Griesbachian), and then increased during the Olenekian and Anisian. Our data support the Lilliput Effect on brachiopods during the Permian-Triassic mass extinction and its immediate aftermath. Size plots at species, genus, and family levels suggest that the earliest Triassic size reduction resulted from two factors: the preferential extinction of large brachiopod taxa (size-selective extinction), and the size reductions in the survivors. Persistent increases in brachiopod size in the Olenekian and Anisian are likely the result of the extinction of small survivors, the appearance of large-sized species and the Cope's rule that the new lineages tend to increase in body size over the early evolutionary time. The cause of the earliest Triassic size reduction of brachiopods might be environmental pressures such as global warming, oceanic anoxia, and increased water turbidity.