We study the scaling behavior of the step scaling function for SU(3) gauge theory, employing the renormalization-group improved Iwasaki gauge action and the perturbatively improved Lüscher-Weisz gauge action. We confirm that the step scaling functions from the improved gauge actions agree with that previously obtained from the plaquette action within errors in the continuum limit at both weak and strong coupling regions. We also investigate how different choices of boundary counterterms for the improved gauge actions affect the scaling behavior. In the extrapolation to the continuum limit, we observe that the cutoff dependence becomes moderate for the Iwasaki action, if a perturbative reduction of scaling violations is applied to the simulation results. We also measure the low energy scale ratio with the Iwasaki action and confirm its universality.