Natural resources accounting is an essential tool in the process of understanding physical flows within the environmental and economic coupling system. It is also an important means to balance regional economic development,environment protection and sustainable development. Physical accounting of environmental pollution is an important part of natural resources accounting. This research reviews the development of environmental physical accounting,drawing on the latest international research and the accounting system of green national accounting experience,and collecting principles of accounting systems at a regional scale. Based on the existing national accounting system and environmental statistics,this research designs the physical accounting system of environmental pollution,including environmental pollution physical accounts,balance sheets,and integrated environmental quality evaluation index. Taking Huzhou,Zhejiang,China as a study case,this research accounts the physical quantity in water environment pollution,and summarizes the advantages and disadvantages of this accounting system. The results show that in order to meet the need of environmental accounting at a regional scale,the designs of physical accounting systems of environmental pollution should follow four principles：compatibility,relevance,orientation and feasibility. In the process of environmental pollution physical accounting,researchers should use the integrated indicators to reflect environment quality,and establish flow accounts to account for pollutants and waste generation,treatment,discharge and consumption in regional economic activity. Using this accounting system will benefit governments,residents,and companies. This requires broad participation and support from regional governments and the community.