Two Elsholtzia haichouensis Sun populations, one from Cu mine sites (Tonglushan) and the other from uncontaminated sites (Hongan) in Hubei province, were investigated in hydroponic experiments for the differences of Cu accumulation and ecophysiological responses to Cu under Cu treatment. The results showed that a significant increase of malondialdehyde (MDA) concentration in roots was observed in Hongan population, whereas no significant change was observed in Tonglushan population. The root pressure exudates (ml) decreased significantly in Hongan population, but increased significantly in Tonglushan population at high Cu concentration (≥20 μmol/L) treatment. Cu concentration in roots of Hongan population was significantly higher than that in Tonglushan population. For example, Cu concentration in Hongan population was 3 times and 4 times higher than that in Tonglushan population after 20 μmol/L Cu treatment for one day and three days, respectively. Cu concentration in Hongan population was 20 times and 5 times higher than that in Tonglushan population after 80 μmol/L Cu treatment for one day and three days, respectively. The intracellular and secreted acid phosphatase activities (APase) in roots were significantly higher in Tonglushan population than in Hongan one. The intracellular APase activities in Tonglushan population were 3 times higher than that in Hongan population after 80 μmol/L Cu treatment for three days and five days; The root secreted APase activities in Tonglushan population were 1.6 times and 1.8 times higher than that in Hongan population after 80 μmol/L Cu treatment for three days and five days. In conclusion, excess Cu caused serious oxidative damage in roots of Hongan population, but not in Tonglushan population. The high activities of intracellular and root-excreted APases in Tonglushan population might play an important role in reducing Cu accumulation in roots and maintaining normal phosphorus physiology metabolism in root cells under Cu stress.