Epibionts and hosts as well as their interactions comprise a special ecosystem in the marine hard-substrate communities which could provide paleoecological implications for the critical events of Earth history. Abundant brachiopod hosts were sampled from the Givetian-Famennian of the Longmenshan region in South China. We describe the encrustation patterns on the brachiopods in terms of epibiont abundance, diversity, relationships between hosts and epibionts, and interaction between epibiont taxa. A total of 3067 brachiopod specimens are examined and identified into seven species, among which 683 specimens are encrusted by epibionts represented by eight taxa. The percentage of encrusted shells and the mean number of epibionts per shell of host brachiopods, are mainly related to the shell morphology of the host and ecological environments. The abundance of epibionts and the number of associations are quite variable among the Middle-Late Devonian stages. Most of epibionts have selective preferences on certain host taxa. The individual size of epibionts is an important factor in choosing the host. During the Givetian and Frasnian time, encrusters were much more abundant on the dorsal valves than on the ventral valves of host brachiopods. However, until the Famennian time, the biconvex spirifemids have more encrusters on the ventral valves. Such an encrusting change from dorsal valves to ventral valves across the F/F boundary might not be related to ecological environments, yet only the change of host taxa. The epibionts encrusted on host brachiopods did not display a sudden collapse around the F-F boundary interval. The epibiont abundance, diversity, relationships between hosts and epibionts, as well as interaction between epibiont taxa do not show a significant change around the F/F boundary. It may indicate there was no dramatic environmental change in the Frasnian and Famennian boundary interval but long-term ecological damage during the Frasnian in the studied region.