Theories beyond the Standard Model often contain mass scales hierarchically different from the electroweak scale and the Planck scale. It has been shown that such hierarchical mass scales can be realized as typical energy scales of multiple 3-branes in a 5D warped spacetime. We present a mechanism for stabilizing the intervals between the multiple 3-branes in the warped extra dimension, by introducing a single 5D scalar field with brane-localized potentials. We discuss the radion stabilization by solving the Einstein equation and the scalar field equation of motion so that a backreaction effect on the geometry due to the presence of the scalar field is taken into account. Perturbations from the background configuration are then considered with proper identification of multiple radion degrees of freedom. By solving their equations of motion, we compute the mass spectrum of the radion-scalar field system and the radion couplings to brane-localized matter fields, which are found to be suppressed by typical energy scales and radion profiles at the branes. We also compute the mass spectrum of Kaluza-Klein gravitons and their profiles in the extra dimension. Some applications of the setup are briefly described. Our analysis provides a solid ground to build 5D warped extra dimension models with multiple 3-branes.