The Rhynchonellida is a major group of brachiopods that survived the “big five” mass extinctions and flourished after the Permian-Triassic (P-Tr) crisis. However, phylogenetic and character evolution in the Rhynchonellida across the P-Tr transition is poorly understood. In view of the widespread homoplasy across this order, we employ a tip-dated Bayesian analysis to reconstruct phylogenetic relationships for Late Permian–Triassic rhynchonellides. The same data were also analyzed using three other methods: undated Bayesian, equal-weighting, and implied-weighting parsimony. Compared with trees generated by other methods, those constructed by tip-dating best account for the homoplasy in this group, and are closer to previous assumptions on the evolution of this group. Based on the analyses of multiple trees, the major increase in lineage richness occurred in the Early and early Middle Triassic, and the richness in the Anisian almost reached its highest level in the Triassic. According to fossil records, a pronounced reduction in shell size and in the development of ornamentation occurred after the P-Tr extinction, which is largely due to the loss of large and highly-sculptured genera, and the diversification of small-sized and weakly-ornamented genera. Ancestral state estimation of shell size and development of ornamentation, coupled with comparisons of other characters, indicate that the Early–Middle Triassic mature “small-sized taxa” may have characters displayed by juveniles of their ancestors. This suggests that for these genera, paedomorphosis was possibly a strategy to survive and diversify in the harsh environment after the P-Tr extinction.