Biochar, typical emerging functional material, has been widely applied for wastewater treatment in constructed wetlands (CWs). However, whether the biochar application can improve the sustainability of aerated CWs, for treating wastewater containing heavy metals, remains needing further clarifying. This study systematically evaluated the effect of biochar addition on the sustainable operation of aerated CWs via typical pollutants removal assessment, enzyme activity evaluation and microbial secretion/structures analyzing. Experimental results revealed that as high as a 92.63% removal rate of NH4+-N, 89.89% for TN and > 95.0% reduction of heavy metals could be achieved in aerated CWs with biochar addition, whereas a significant decreasing of nitrogen removal (NH4+-N: 74.58%; TN: 58.52%) was observed with the existence of Cr and Cu in influent. Biochar addition led to a significant increase of extracellular polymeric substance (from 122.8 to 218.9 μg g−1 gravel−1) and a noteworthy variation of biochemical compositions of plants, revealing an increasement of clogging risk and enhancement of stress of heavy metals on wetland plants. The dynamics transformation of microbial structures indicated that the utilization of biochar could amplify the toxicity to the Betaproteobacteria and Alphaproteobacteria, subsequently negative affected the nitrogen-cycle. Correlation analysis and heavy metal speciation indicated that Cr (especially organic-bound fraction and Fe-Mn oxide-bound fraction) would affect the nitrate reductase activity related to the denitrification process, while Cu influenced the transformation of NH4+-N via ammonia monooxygenase activity. Overall, utilization of biochar posed a hidden therapy to sustainability of aerated CWs for treating wastewater containing heavy metals.