The Satoyama landscape in Japan is the conservation hotspot of biodiversity and ecosystem services. Agriculture intensification, especially the consolidation of agricultural facilities of irrigation and drainage systems, cropland levees and roads, resulted in the fragmentation and homogeneity of species habitats and eventually caused the losses of biodiversity and ecosysem serveses. Taking Tochigi prefecture in Japan as study area, we propose the agricultural intensification index,the habitat diversity index and the distribution of redlist species as biodiversity indicator, we analyze the relationships between agricultural intensification and biodiversity. The results show it is not obvious that the transformation between non-agricultural and agricultural habitats. The impacts on biodiversity varied with the different aspects of agricultural intensification. Future research should focus on the spatial scale of impacts on biodiverstiy by agricultural intensification.