If the waste water, waste gas, noise and solid waste produced in the process of natural gas exploitation are not properly controlled, it will have an impact and threat on the ecological environment. Carrying out the supervision of ecological environment protection is an important means to improve the enterprise's ecological environment management and promote the implementation of ecological environment protection measures. In this regard, this paper expounds the pollution producing links of natural gas drilling, gas production, gathering and transportation and purification. Combined with the elements of environmental protection management, it puts forward the supervision contents of ecological environment protection for natural gas mining enterprises, including the implementation of Xi Jinping's ecological civilization ideology, the implementation of pollutant discharge permit, the environmental impact assessment of construction projects and the "three simultaneous" compliance management, environmental risk management and control, and hidden trouble management. Clean production and greenhouse gas control, pollution control, environmental protection training and statistics, etc. According to the characteristics of natural gas exploitation industry, the supervision methods and suggestions of "check", "see", "ask", "listen", "perform", "test", "test" and "record" are summarized, and the supervision mode of ecological environment protection is proposed, which combines standardized supervision with intelligent and information supervision, and uses special supervision, daily supervision and multi-level supervision.