Land use change is one of the main drivers of biodiversity loss. In the last 20 years, China’s land use pattern has undergone profound changes. This study constructs an Ecosystem Comprehensive Anthropogenic Disturbance Index(ECADI) to assess disturbance impacts of land use change between 1990 and 2010 on biodiversity conservation priority areas at national and regional scales. Four levels of biodiversity conservation areas were categorized: generally important areas, moderately important areas, important areas, and very important areas. The results indicated a higher ECADI value in 2010 in Central and Eastern China than in Western China, and the values of the moderately important, important and very important regions were lower than the average value of the whole country at all levels. Notably, in recent 20 years, the change extent of ECADI values in Central and Eastern China were much greater compared with that in Western China, and ECADI values in the moderately important, important and very important biodiversity conservation areas all showed increasing trends, with the increasing extent lower than that of whole China at all levels. Due to human activities such as urbanization in Eastern China and cropland reclamation in Northeast China and Xinjiang, ECADI values showed a medium increase trend(the change rate was about 1%–5% in 10 years), which indicated the need for more conservation efforts in those regions. However, ECADI values in the Loess Plateau presented a low decline trend(the change rate was about –1% to –0.1% in 10 years) after 2000 because of the obvious effectiveness of Green for Grain Project. Furthermore, the variation was negligible in the Tibetan Plateau.