More than ten percent of people suffer from at least one episode of depression and related mental disorders in a lifetime, and depression and related mental disorders are one of the world’s greatest public health problems. A multiple system theory holds that dysregulation of the multiple systems underlies the pathogenesis of depression and related mental disorders, and new therapies based on the multiple system dysregulation theory are urgently needed. In this study, the antidepressant effect of decoction from herb Cistanche deserticola Y.C.Ma and Cistanche tubulosa was examined. Herb Cistanche decoction reduced the immobility period significantly in the mouse tail suspension test. Mice treated with herb decoction showed an improved ability of spatial learning and memory in the Morris water maze test. Groups treated herb decoction displayed a downregulated monoamine oxidase (MAO) activity; the dopamine (DA) concentration in the brain was upregulated, indicating herb Cistanche decoction improved the nerve excitability; the serum concentration of corticosterone (CORT) was downregulated, showing that mice benefited from a reduced stress level. Hence, the antidepressant efficacy and mechanism of traditional Chinese herb Cistanche were explored in this study. Herb Cistanche showed a potential to be developed as a complementary and alternative therapy for depression.