The "Two Mountains" concept has promoted the understanding of and attention to the ecological value of governments at all levels in China. The research and application of natural capital accounting in the global academic circle has entered a new stage. How to transform research analysis into management system and make the evaluation of ecosystem regularly in governmental mechanism, become a new research topic. In response to the requirements of the central government, Shenzhen actively carried out ecosystem service value accounting and service ecological governance, and took the lead in formulating the first government Gross Ecosystem Product (GEP) accounting system in China (and even the world). This paper introduces the construction process of the GEP accounting system and describes the main characteristics of the GEP accounting in Shenzhen City. The results of Shenzhen GEP trial calculation during the "13th Five-Year Plan" period (2016-2020) are presented. We also discuss the application path of Shenzhen GEP in urban governance.