To reveal the similarities and differences in the resistance mechanisms of different ecotypes to Cu stress, a pot experiment was used to systematically compare the physiological responses of non-mining ecotype Miscanthus floridulus (collected from Boluo County, Huizhou City) and mining ecotype Miscanthus floridulus (collected from Dabaoshan mining area) under different Cu concentrations. The results showed that chlorophyll a, chlorophyll b and total chlorophyll in the leaves of the two ecotypes of M. floridulus were negatively correlated with Cu stress concentration (p < 0.01), but the extent of decrease for the ecotypes in the mining area was lower than that for the ecotypes in the non-mining area. The values of chlorophyll a/b for both ecotypes increased with increasing Cu treatment concentration, indicating that Cu is more harmful to chlorophyll b than to chlorophyll a for M. floridulus. Cu stress can lead to the accumulation of malondialdehyde (MDA) in the leaves of M. floridulus with the amount of MDA accumulation observed being greater in the non-mining ecotype than in the mining ecotype (p < 0.05). The content of antioxidant substances (ascorbic acid and reduced glutathione) in the mining ecotype M. floridulus was significantly higher than that in the non-mining ecotype. The activity of SOD in the leaves of non-mining ecotypes was inhibited by Cu stress and the activity of POD was increased by Cu stress. However, the increase in POD in the mining ecotypes was greater than that in the non-mining ecotypes and the activities of the two enzymes in the mining ecotypes were significantly higher than those in the non-mining ecotypes at the highest concentration of Cu. Cu had different effects on PPO activity in the leaves of the two ecotypes of M. floridulus. The plant leaves of the non-mining ecotype at 400 and 800 mg·kg−1 were significantly fewer than those of the control group (p < 0.05), which were 87.1% and 65.2% of the control group, respectively. The PPO activity in the plant leaves of the mining ecotype was higher than that in the leaves of the non-mining ecotype and was significantly higher at 400 and 800 mg·kg−1 than that of the control group (p < 0.05), at 226.5% and 268.1% of the control group, respectively. These results indicate that the mining ecotype M. floridulus is more resistant to copper stress, that resistant ecotypes have been formed, and that small-molecule antioxidant substances play an important role in increasing resistance levels.