A heavy metal resistant strain F1 was isolated from the mining area of the Fuyun county, Xinjiang. The contents of the chlorophyll a, soluble protein, MDA and glutathione (GSH), and enzyme activity of the glutathione stransferase(GST), glutathione peroxidase (GSHPX) and glutamylcysteine synthase (GCL) were measured while the strain F1 exposed to the different concentrations（0, 0.5, 1.0, 1.5 and 2.0 mmol/L） of Cu²⁺; subsequently, the functional groups involved with the heavy metal chelating process and the data related to cell wall ion exchange process were determined using infrared spectrometer and scanning electron microscope, respectively. As the results, (1) soil microalgae F1 exhibited relatively high tolerance capability against Cu²⁺stress; (2) OH, CH₂, RCONH₂ and COH were confirmed as the key participants of the stress tolerance process; (3) the absorption process of Cu²⁺ was done by exchanging other positive ions, such as Al³⁺, Fe²⁺, Mg²⁺, Ca²⁺, K⁺, Na⁺ and Zn²⁺; (4) in algae cells，GSH and GSHPX were the essential factors which have important role against Cu²⁺ stress. In conclusion, the fine structure of cell wall and its ion exchange ability were the fundamental factors in Cu²⁺ tolerance; in particular, those chemical groups that were examined above. Moreover, the glutathionerelated enzymes protected the cell from internal damage by preventing the active oxygen from excess accumulation, so that, protects the cell damage under the stress.