Development of substrate organisms (oysters, barnacles) and the health of a monitored oyster reef were investigated in the Yangtze Estuary. Very low salinity suppressed oyster survival. Nevertheless, middle- to high-salinity significantly increased the abundance and biomass of substrate organisms, and macrobenthos species and diversity. Long-term variation in substrate organisms was steady after a major fluctuation, yet the macrobenthic community structure lagged behind that of oysters. Overall, the oyster reef was in a healthy state. The M-AMBI results showed that its ecological status under high-salinity was better than medium-salinity conditions. Redundancy analysis indicated these results were associated with changes in water salinity and substrate factors. Taken together, our results suggest this constructed intertidal oyster reef has had a positive effect on the community and health status of macrobenthos in the Yangtze Estuary. Further, these ecological benefits increased going from medium- to high-salinity waters, but were generally absent under low salinity.