Traditional metal toxicity tests on organisms have mainly focused on continuous exposure at a fixed concentration. However, organisms are more likely exposed to pollutants intermittently in estuarine environments that are significantly impacted by anthropogenic activity. The present study examined whether different copper (Cu) exposure regimes at an equivalent dose can induce different metabolomics effects on the oysters. An estuarine oyster Crassostrea hongkongensis was exposed to Cu continuously or intermittently at an equal dose (time × concentration) for 6 wk. Continuous exposure regimes included 2 doses of 3.3 μg/L for 24 h and 20 μg/L for 24 h, with corresponding equal doses of 2 intermittent exposure regimes of 20 μg/L for 4 h and 120 μg/L for 4 h, respectively. Time-course measurements suggested that Cu bioaccumulation was comparable at equal low doses between the continuous regime (3.3 μg/L for 24 h) and the intermittent regime (20 μg/L for 4 h), but there was considerable difference for the high dose under different regimes. Nuclear magnetic resonance (NMR)-based metabolomics suggested that continuous and intermittent Cu exposures led to similar metabolite variation pattern in gills at an equal high dose, including decreased amino acids (e.g., aspartate, glycine, isoleucine, leucine, lysine, phenylalanine, threonine, and valine), lower energy-related compounds (e.g., adenosine triphosphate/adenosine diphosphate, acetate, citrate, and glycogen), and altered osmolytes (e.g., homarine and taurine). These biomarkers indicated disturbance of osmotic regulation and energy metabolism induced by Cu exposure regardless of regime. In addition, the 4-h intermittent Cu exposure resulted in slightly fewer adverse effects compared with the corresponding equal-dose continuous exposure. Oysters appeared to recover during the intervals of Cu exposure. The results indicated that metabolomic effects induced by Cu were more dose dependent than the Cu exposure regime. Environ Toxicol Chem 2017;36:2428-2435. © 2017 SETAC.