Abstract To compare the roles of two kinds of initial perturbations in a convection-permitting ensemble prediction system (CPEPS) and reveal the effects of the differences in large-scale/small-scale perturbation components on the CPEPS, three initial perturbation schemes are introduced, including a dynamical downscaling (DOWN) scheme originating from a coarse-resolution model, a multiscale ensemble transform Kalman filter (ETKF) scheme, and a filtered ETKF (ETKF_LARGE) scheme. First, the comparisons between the DOWN and ETKF schemes reveal that they behave differently in many ways. Specifically, the ensemble spread and forecast error for precipitation in the DOWN scheme are larger than those in the ETKF; the probabilistic forecasting skill for precipitation in the DOWN scheme is better than that in the ETKF at small neighborhood radii, whereas the advantages of the ETKF begin to appear as the neighborhood radius increases; DOWN possesses better spread–skill relationships than ETKF and has comparable probabilistic forecasting skills for nonprecipitation. Second, the comparisons between DOWN and ETKF_LARGE indicate that the differences in the large-scale initial perturbation components are key to the differences between DOWN and ETKF. Third, the comparisons between ETKF and ETKF_LARGE demonstrate that the small-scale initial perturbations are important since they can increase the precipitation spread in the early times and decrease the forecast errors while simultaneously improving the probabilistic forecasting skill for precipitation. Given the advantages of the DOWN and ETKF schemes and the importance of both large-scale and small-scale initial perturbations, multiscale initial perturbations should be constructed in future research.