Based on the introduction of the development history of environmental impact assessment on basin comprehensive planning and conception connotations of environmental impact assessment index system, a comprehensive analysis to Nanpan River Basin was made. Combined with practical experiences, a conception model of impact identification was set up starting from resource system and environmental system. A basic model of resource-environment was used to identify the environmental impact, determine the environmental protection objectives, and formulate corresponding index control values, forming a multi-hierarchy index system at last to provide technical basis and supports for the establishment and application of environmental impact assessment on basin comprehensive planning in the future.