The present invention relates to a compound of Antrodia camphorata used to treat autoimmune diseases, in particular to an extract, 4-hydroxy-2,3-dimethoxy-6-methyl-5(3,7,11-trimethyl-dodeca-2,6,10-trienyl- )-cyclohex-2-enone, isolated from Antrodia camphorata, and its use in alleviating symptoms of autoimmune diseases such as systemic lupus erythematosus (SLE). The cyclohexenone compound according to the present invention helps to decrease proteinuria levels and antinuclear antibody titers in SLE mammals in order to alleviate kidney inflammation and disease, as well as the self-damage caused by antinuclear antibodies. The purpose for prevention and treatment of autoimmune diseases and kidney diseases by the natural, side-effect free substance can then be accomplished.