Green GDP represents the net positive effect of national economic growth. The positive effect of national economic growth will be enhanced if there is a higher percentage of green GDP in GDP. From the perspective of resources and environment, this paper introduces SEEA-2012 accounting system with indirect calculating methods of green GDP in China, within which the value of natural resource depletion, environmental pollution damage and environmental quality degradation are included. In order to reasonably select valid indicators and data so as to get accurate accounting results, different valuation methods and operational formulas in economics are adopted to construct a new accounting system model, and the green GDP of Chongqing City in 2018-2020 is accounted for. Results show that the green GDP of Chongqing in recent three years is 1,838.889 billion Yuan, 1,964.724 billion Yuan and 2,111.2 billion Yuan, respectively, and proportions of green GDP in traditional GDP are 90.30%, 91.01% and 89.44% respectively. By studying and analyzing the dependence of Chongqing on natural resources and the ecological environment in the process of economic development, this paper provides theoretical support for the sustainable development of the urban economy and environment, provides a reference basis for the local government to formulate economic development planning, and also provides a reference for the construction of green GDP accounting system in similar ecological areas.