To reduce ecological environmental pollution and economic loss, and improve national environmental awareness, this paper puts forward the optimization of China's ecological tax system based on the GEP development strategy. Firstly, the analysis shows that GDP focuses on economic operation, while GEP focuses on ecosystem operation. Then, GEP is used to calculate the data of water conservation, soil conservation function, flood regulation and storage, air and water purification, carbon fixation and oxygen release, climate regulation, biological community, and other indicators to obtain the corresponding value. We will use fiscal principles to adjust the sensitivity of economic changes, the principle of fairness to narrow income disparities, and the principle of efficiency to adjust market collection and management, simplify the tax system, and improve national treatment. Finally, the maximization of tax benefits is realized with the minimum tax cost under the tax system. Through experiments, it is proved that this method can effectively explore the development of an ecological tax system, to optimize the overall optimization of tax collection and management up to 0.77.