Ecosystem was typical opening energetics system, and had a dissipative structural character. Energetics entropy’s mechanism of biodiversity was described. Two entropy’s measure indexes were put forward. The meaning of each index, correlativity of two entropy’s indexes and mechanism corresponding of entropy and popular measure index were in-depthly analyzed in detail. Investigated data of Tianmu Nature Reserve’s model sample were tested. The result were consistent to mechanism of entropy. New thought and method were provided to research of biodiversity. Measure indexes of biodiversity were generally popular and old, three applied examples were compared and analyzed. Disfigurement of popular measure index was displayed. It was observed that popular measure index did not consider the genus’s number which affected to biodiversity in the community. Entropy of popular measure index improved was put forward. This paper finally analyzed several key issues about entropy, and primary factors which influenced Biodiversity of Tianmu Nature Reserve.