The end-Triassic mass extinction (ETME) is considered to be one of the five most severe extinction events in Earth history and caused the disappearance of ca. 80% of all species. The terrestrial ecosystems were also greatly affected by this extinction, but the severity of the land plant diversity loss is not well understood. Ferns are once a principal component of the terrestrial ecosystem from the late Paleozoic/early Mesozoic era and colonizers taxa commonly found in disturbed environments. In this study, we investigated the diversity and ecology of fern during the Triassic-Jurassic (Tr-J) transition in the Sichuan Basin of South China and focused for the first time on the impact of the end-Triassic mass extinction event on the fern communities. We assembled fern fossil records in 16 localities from the Rhaetian Xujiahe (XJH) Formation to the lowermost Jurassic Zhenzhuchong (ZZC) Formation. Our results indicate that no obvious mass extinctions of macro-microflora of ferns but a clear species turnover was recorded at ETME in the Sichuan Basin, reflected an appropriate response of plants in places far away from CAMP volcanism. The paleoecological analysis based on macroflora and microflora in the Sichuan Basin shows a warm and humid condition of tropical-subtropical climate during Rhaetian followed by an increase of specific dry-resistant taxa, indicating a dryer environment at the Earliest Jurassic. Additionally, multivariate statistical approaches (principal coordinates analysis, cluster analysis, network analysis) for fern macro-remains and spores data in the southeastern Sichuan Basin infer that the members of XJH and ZZC Formation cluster in three groups, corresponding to their environmental conditions, determined by humidity and temperature.