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Afforestation is a primary response to the loss and degradation of mangroves worldwide. The successful restoration of mangrove ecosystems is in part indicated by the rebuilding of macrobenthic community. However, the community dynamic of benthic macrofauna after mangrove afforestation was poorly known. Here, three quarterly surveys (2006–2007, 2014–2015, 2019–2020) of the benthic macrofauna and sediment grain size were conducted in a mix-planted mangrove stand (Kandelia obovata + Sonneratia apetala) in Xiamen Tong'an Bay, China. Our results showed that the community structure of benthic macrofauna differed significantly after mangrove afforestation. These differences were accompanied by the declines in the species number, abundance, biomass, and diversity (H'), as well as the fining of sediments. We also found that the epifauna and infauna exhibited different adaptabilities to mangrove vegetation. Additionally, shifts in the composition of the functional feeding groups were observed, indicating the modification of trophic structure after mangrove afforestation. We recommend that future mangrove afforestation programs call for a guide to coordinate habitats for different taxa.