As an important component of the EU’s “Fit for 55” package, Emission Trading System II (ETS2) is designed to drive emission reductions in sectors including road transport and buildings. To explore how the ETS2 policy affects carbon emission within the road transport sector, this study develops a tripartite evolutionary game model involving government, fuel suppliers, and road transport enterprises to compare strategic evolution under Energy Taxation Directive (ETD) policy and the combined policy that includes ETD and ETS2, and further examines how green fuel prices and carbon price affect strategy choices and the equilibrium of whole system. The results show that, compared with the standalone ETD policy, the ETD+ETS2 combined policy more effectively strengthens the endogenous motivation of fuel suppliers and road transport enterprises for green transition. When green fuel prices remain within a reasonable range, fuel suppliers tend to choose green transformation, while road transport enterprises tend to choose green operation. However, as the carbon allowance price or the energy tax on green fuels increases from low to high levels, fuel suppliers shift from green transformation to conventional production. These findings provide a theoretical reference for the coordinated design of EU’s ETD and ETS2 policies and for enterprise emission-reduction strategies.