Taxation is the core element that guides and promotes the upgrading of industrial structure, industrial structure ecologisation is an important part of realising green development, and evaluating and optimising the effect of taxation is of great significance to realising green development. Based on the analysis of the influencing factors and the mechanism of industrial structure ecologisation, a theoretical framework model of industrial structure ecologisation was established, and based on the theoretical model, a two-way fixed-effect regression model, a panel threshold model, an intermediary effect model and other econometric models were constructed, and the effect of taxation on industrial structure ecologisation was empirically analyzed. Corresponding optimisation suggestions are put forward in terms of perfecting the tax system and optimising the innovation environment.