Abstract: It is an important milestone of the greening tax systems in China that the Environmental Protection Tax Law has been employed and enforced. Differing from the financial accounting in the past, the taxation basis for the environmental protection tax is the pollution equivalents, pollutant discharges and decibels, which the taxation authority cannot deal with efficiently. Based on the theory of holistic government, the ecology and environment authority, which has undertaken the duty of environmental monitoring and pollution abatement for a long time, was introduced into the tax collection and management for the purpose of overcoming the inexperience and poor performance of hte taxation authority, improving the efficiency of environmental protection tax collection and management through cross-sector collaboration. However, that is an ideal state. In fact, the difficulties and obstacles in the mode of cooperation in tax collection and management between the two authorities has restricted the effect of environmental protection tax, such as unclear functional division, inappropriate duty coordination and lack of incentive mechanism. To achieve the goal of enhancing the quality and effectiveness of tax collection and management, the system of environmental protection tax collection and management should specify the equal status of the taxation authority and the ecology and environment authority in the cooperation, clarify their respective responsibilities based on the goal of efficiency of a holistic government, and establish the scientific and long-term mechanism for environmental protection taxation by regulating the distribution and use of revenues and stimulating the enthusiasm for cross-sector collaboration.