We study the thermodynamics of the SU(3) gauge theory using the fixed-scale approach with shifted boundary conditions. The fixed-scale approach can reduce the numerical cost of the zero-temperature part in the equation of state calculations, while the number of possible temperatures is limited by the integer $N_t$, which represents the temporal lattice extent. The shifted boundary conditions can overcome such a limitation while retaining the advantages of the fixed-scale approach. Therefore, our approach enables the investigation of not only the equation of state in detail, but also the calculation of the critical temperature with increased precision even with the fixed-scale approach. We also confirm numerically that the boundary conditions suppress the lattice artifact of the equation of state, which has been confirmed in the non-interacting limit.