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The environmental protection tax is an important tool for China to deal with environmental problems when the country' s environmental governance faces severe challenges. China' s current environmental protection tax system is largely an extension of the sewage charging system. There are some problems, such as the need to adjust the tax base, unreasonable tax rates, imperfect preferential policies, and the need to improve the efficiency of tax collection and management. Comprehensively evaluating the impact of environmental protection tax and optimizing the design of the environmental protection tax rate from the perspective of economic, environmental, and innovation synergy is of great value to improving China' s environmental governance system and realizing the transformation of the green economy. This study theoretically analyzed the impact of environmental protection tax on enterprise development; constructed a simulation model to analyze the impact of environmental protection tax; and numerically simulated the comprehensive impact of different environmental protection tax implementation intensity (IEPT) from 2006 to 2019 by using the mixed data of Chinese micro-enterprises and provincial panels and the scenario analysis method to predict the multi-dimensional impact of environmental protection tax in 2030. The results showed that: ① From 2006 to 2019, China' s environmental protection tax rate was at a low level, which was less than the optimal IEPT. The relationship between the optimal IEPT and the synergy index was 'inverted-U' shaped; that is, with the continuous rise of IEPT, the synergy index also showed the trend of rising first and then fluctuating and declining. ② Over time, the optimal IEPT showed an overall upward trend. ③ When the development level and demands of the economy, environment, and innovation became different, the optimal IEPT would also change. Finally, this study puts forward policy suggestions for China' s environmental protection tax reform: ① After fully investigating the operation status and innovation development status of regional inter-industry enterprises, we should consider further refining regional and industrial heterogeneous pricing strategies within the scope of regional environmental carrying capacity. ② A dynamic adjustment mechanism for the tax rate of environmental protection tax should be established to gradually increase the tax rate and give full play to the policy effect of environmental protection tax. ③ The environmental protection tax should be used to establish a special fund for innovation support, to avoid bringing higher environmental costs to innovative enterprises due to the increase in the environmental protection tax rate. [ABSTRACT FROM AUTHOR]