The Late Devonian biotic crisis has been studied for a long time mainly on the basis of its taxonomic severity, but with little attention paid on the relationship between biogeography and evolutionary dynamics. In this study, brachiopod faunas across the biotic crisis are surveyed based on revised data compiled from 15 sections in South China. Data of brachiopod faunas are plotted using a network method to detect biogeographic variation and dynamics through the upper Frasnian, lower and middle Famennian. In addition, frequency analysis is performed on the occurrence of brachiopod faunas within the different localities and depositional settings through time. These data show significant taxonomic loss in the five depositional zones in South China, particularly in the littoral clastic and restricted-platform facies. Refuges during the survival interval were probably located in deeper water zones, especially in the inter-platform basin, but also in the peritidal and the open carbonate platform. A decrease of biogeographic connections within the brachiopod occurrence network, accompanied with an increase of low frequency taxa in the survival and recovery intervals, supports biogeographic divergence of ecological preferences of survival and recovery faunas in South China, as well as a turnover of brachiopod faunas through the biotic crisis. Reasons for variation of biogeographic distribution and connections are less known, besides the faunal colonisation that facilitated by sea-level fluctuation through the biotic crisis.