The environment is the foundation of human survival and development. Environmental performance audit in the relationship between coordinated development and environmental protection is of great significance. Standing on the ground of government audit to guide regional development from macro level, analyzing the influence of purposes and contents of audit on the construction of audit indicator system, this paper finds out that the audit indicator system is divided into three dimensions: environmental quality indicators, interaction between environment and development indicators and decision-making and action indicators. The three mutually driven dimensions work together to reach a sustainable development. Through breaking down each dimension respectively according to the environmental elements，direction of interaction between environment and development and governmental responsibilities step by step, a feasible environmental performance audit indicator system is built up, which plays a guiding role on improving the quality of regional development.