Abstract: This paper sets up a set of index system of impact assessment of social economy change to biodiversity, and puts forwards the train of thought, principles, content and structure levels of the system from the aspect of strategic environmental assessment(SEA). Index weight of each level is calculated using analytic hierarchy process(AHP) method. Taking Water Diversion Project of Central Yunnan Province as an example, empirical study on the effects of social economy change to biodiversity is carried out by choosing three areas in central Yunnan province as cases. Results show that the index system can reflect the affect of social economy change to biodiversity in the region.