Subterranean environments are essential for the survival of many bat species and other cave fauna but these places are subject to increasing human disturbance. To examine the significance of subterranean habitats for the conservation of bats in China we surveyed bat species in 225 underground sites during 2003–2011. Our results show that 77% of bat species in China, including 30 nationally Endangered or Vulnerable species and nine endemic species, roost in caves and other subterranean habitats. The number of species in occupied roosts was 1–15. Almost 90% of the roosts surveyed contained signs of human disturbance, most of which was from recreational activities. One hundred and twenty-one roosts merit special concern because they harbour ≥ 6 species or > 1,000 individuals, or species of special concern (threatened or endemic species). Generally, larger roosts support more species and a greater abundance of bats than smaller roosts but there is no direct correlation between the presence of species of special concern and roost size. Disused tourist caves have significantly more bat species than other types of roosts. Our data demonstrate that roost disturbance by recreational activities has pronounced detrimental effects on the number of bat species and the presence of species of special concern. We discuss the social, economic and political issues that could adversely affect bat conservation in caves in China, and we recommend that protection of subterranean habitats should be a high priority for bat conservation.