Regional ecological risk assessment (regional ERA) was characterized by multiple risk stressors, receptors and endpoints with uncertainty and spatial heterogeneity, and it was distinct from traditional risk assessment in sources, stressors and scales. A framework of regional ERA based on terrestrial ecosystem was established in this paper. A number of major emerging issues in regional ERA such as uncertainty analysis, difficulties in scale extrapolation, disunity of assessment indicators and standards, identification and prioritization of risk factors, mixed pollution in a certain region, transition from aquatic ecosystem to terrestrial ecosystem risk assessment and special human factors were illustrated. In addition, a couple of methods, theories and tools for analyzing these issues in regional ERA were recommended as well. At last, prospects for regional ERA were proposed with emphases on risk monitoring and data collection and processing, integration of index system, new methodology, spatial characterization and expression, feedback and risk management mechanism for regional ERA.