In recent years, the rising environmental loading ratio indicates an increasing pressure of economic activities on the environment, and the economic development achieved at the cost of over-exploitation of resources and environment deterioration. The development of regional economy is becoming a sharp contradiction with ecological environment and resources conservation. In some regions, economic issues and environmental problems have become major social focus. We have been using GDP to measure the level of economic development for a long time. However, economic growth cannot be achieved without the consumption of resources and environment. It is necessary to explore a method that can correctly measure the relationship between the economic development (including the quality and quantity of economic development) and the resource and environment consumption. This will make a great contribution to the protection of resources and environment. Currently, there are lots of researches of Green GDP, and some countries have gradually built up resource checking account, but the accounting methods of Green GDP are not uniform, and the accounting system has some defects. This paper provides an integrated study on the Green GDP account for Shangluo City in Shaanxi Province from 2003 to 2012 based on Emergy Synthesis Theory. An emergy-based multiple spatial scale analysis framework and a rigorous accounting method that can quantify the values of human-made and natural capital losses were proposed in this study. The advantage of Emergy Theory Method is that it has unified dimension measuring unit for natural and environmental resource, and there are more index range can be selected to expand. The green GDP accounting tends to be more accurate, more reasonable and scientific. According to Odum’s emergy theory and method of economic system, we conduct a research on quantitative Green GDP accounting for Shangluo City from 2003 to 2012. We find: 1) The GDP values of Shangluo from 2003 to 2012 are between 1.12×109 and 6.72×109 $; the green GDP in the same years are in the range of 9.80×108-3.35×109 $; and green GDP/GDP (%) are at 49.85%-87.50%. 2) From 2003 to 2012, along with the development of economy in Shangluo City, the consumption of natural resources and environment resources increased quickly, resulting the green GDP varied greatly from 2003 to 2012. The annual consumption of environmental resources accounted for 5.18%-24.39% of GDP, and the effect of the environmental resources value loss is greater than that of the loss of natural resource on the green GDP accounting in 2008 and 2009, while it is on the contrary in the rest of the years. 3) Input resources, include petrol, diesel oil, chemical fertilizer, pesticide etc, have little effect on the green GDP accounting, accounting 0.83%-1.30% of GDP every year. In short, because of the excessive dependence on resources and the environment, the economic development model of Shangluo is not sustainable, which will get the local economy into a vicious spiral. In addition, green GDP accounting based on Emergy Theory shows great advantage, and regional transmission of various ecological flows is one of the biggest challenges in further studying.