© 2017, Society of Wetland Scientists. Constructed wetlands (CWs) for wastewater treatment had drawn much attention for their additional function of conserving freshwater ecosystems. The purpose of this study was to evaluate the macroinvertebrate biodiversity of two subsurface-flow and surface-flow hybrid CW systems (Qimei CW system (QCWS) and Kejiyuan CW system (KCWS)) under high and low pollutant stress in China. Nonmetric multidimensional scaling (NMDS) and canonical correspondence analysis (CCA) were used to analyze the water quality and aquatic macroinvertebrates community data. The results indicated that the subsurface-flow CW could conserve significant macroinvertebrate biodiversity (total taxon richness 17). The community structure was influenced by habitat types (i.e., subsurface-flow vs. surface-flow CWs) under low pollutant stress, and this influence was somehow masked by influence of water quality under high pollutant stress. Good pollutant removal rates were obtained in decreasing the concentrations of total nitrogen (66.37% and 27.28%), total phosphorus (58.93% and 37.55%), and loadings of biochemical oxygen demand (28.38% and 73.71%) in QCWS and KCWS, respectively. This study implied that subsurface-flow CWs could achieved good performance in both water purification and biodiversity conservation, which could provide a more solid basis for the application of subsurface-flow CWs.