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The degradation of marine habitats (especially coral reefs) and the loss of marine fauna can be mitigated by the construction of artificial reefs (ARs). Macrobenthic fauna are considered excellent indicators of how disturbance or succession affects ecosystems, but the integrated effects of AR construction on taxonomic and thermodynamic indicators of macrobenthic faunal communities have seldom been studied. In the current study, we investigated changes in the taxonomic diversity and ecological exergy (eco-exergy) of the macrobenthic faunal community for 2 years following AR construction in Daya Bay, China. The results indicated that macrobenthic faunal diversity, species richness, and evenness increased but abundance, biomass, eco-exergy, and specific eco-exergy decreased following AR construction; after declining, however, abundance, biomass, and eco-exergy appeared to be increasing at the end of the 2-year sampling period. In terms of biomass and eco-exergy, mollusks were the dominant group at each sampling period and were mainly responsible for the changes in biomass and ecoexergy. Eco-exergy was positively correlated with macrobenthic abundance and was negatively related with evenness. Effects of AR construction on the nearby non-reef habitat were similar to those on the AR habitat. These results indicate that long-term assessment of multiple ecological indicators at diverse study areas is needed to determine the effects of AR construction on marine biological resources.