A high temperature-tolerating thermoacidophilic archae (TA) was isolated from water samples collected from a hot sulfur-containing spring in the Yunnan Province, China, and was used in bioleaching experiments of a low-grade chalcopyrite ore. The TA grow at temperatures ranging from 40 to 80℃, with 65℃ being the optimum temperature, and at pH values of 1.5 to 4.0, with an optimum pH value of 2.0. The bioleaching experiments of the chalcopyrite ore were conducted in both laboratory batch bioreactors and leaching columns. The results obtained from the bioreactor experiments showed that the TA bioleaching rate of copper reached 97% for a 12-day leaching period, while the bioleaching rate was 32.43% for thiobacillus ferrooxidans (Tf) leaching for the same leaching time. In the case of column leaching, tests of a two-phase leaching (196 days), that is,a two-month (56 days) Tf leaching in the first phase, followed by a 140-day TA leaching in the second phase were performed. The average leaching rate of copper achieved for the 140-day TA leaching was 195mg/(L· d), while for the control experiments, it was as low as 78mg/(L· d) for the Tf leaching, indicating that the TA possesses a more powerful oxidizing ability to the chalcopyrite than Tf. Therefore, it is suggested that the two-phase leaching process be applied to for the heap leaching operations, whereas, the TA can be used in the second phase when the temperature inside the heap has increased, and the primary copper sulfide minerals have already been partially oxidized with Tf beforehand in the first phase.