Reducing the cost of pollution control during exploitation of shale gas is of great significance for achieving sustainable development of energy and environmental. This paper takes the cost control of pollution control in the exploitation process of shale gas as the research objective, constructs the accounting system of pollution control cost in the exploitation process of shale gas and establishes the systematic measurement model of environmental cost. The M shale gas company is taken as an example and conducts the case analysis of the cost control of pollution control in the exploitation process of shale gas. The research results show that the pollution control cost in the exploitation process of shale gas includes environmental prevention and control cost and environmental damage cost. Through the analysis of the cost control result of M company Analysis, it realizes the internalization of external cost. This study provides references for shale gas companies to achieve scientific management and control decision-making of environmental costs and is of certain practical significance.