Human disturbances are greatly threatening to the biodiversity of vascular plants. Compared to seed plants, the diversity patterns of ferns have been poorly studied along disturbance gradients, including aspects of their taxonomic, phylogenetic, and functional diversity. Longnan County, a biodiversity hotspot in the subtropical zone in South China, was selected to obtain a more thorough picture of the fern–disturbance relationship, in particular, the taxonomic, phylogenetic, and functional diversity of ferns at different levels of disturbance. In 90 sample plots of 5 × 5 m2 along roadsides at three sites, we recorded a total of 20 families, 50 genera, and 99 species of ferns, as well as 9759 individual ferns. The sample coverage curve indicated that the sampling effort was sufficient for biodiversity analysis. In general, the taxonomic, phylogenetic, and functional diversity measured by Hill numbers of order q = 0–3 indicated that the fern diversity in Longnan County was largely influenced by the level of human disturbance, which supports the ‘increasing disturbance hypothesis’. Many functional traits of ferns at the most disturbed site were adaptive to the disturbance. There were also some indicators of fern species responding to the different disturbance levels. Hence, ferns may be considered as a good indicator group for environmental stress.