Endophyte widely distributed in medicinal plants, it and its host medicinal plants formed a mutually beneficial symbiotic relationship in the long-term co-evolution process. Endophyte could produce a variety of active substances, and played a catalytic role in the medicinal plant growth, stress resistance and the yield accumulation of active ingredient which having important application on medicine and biological control. The isolation of endophytes in medicinal plant and the function of active substances were summarized in the paper.