We investigate a simple 5D extension of the Minimal Supersymmetric (SUSY) Standard Model (SM) that is combined with the bulk matter Randall-Sundrum (RS) model, which gives a natural explanation the Yukawa coupling hierarchy. In this model, matter and gauge superfields reside in the 5D bulk while a SUSY breaking sector and the Higgs doublet superfields are localized on the infrared brane. The Yukawa coupling hierarchy in SM can be naturally explained through the wavefunction localization of the matter superfields. While sparticles obtain their flavor-blind soft SUSY breaking masses dominantly from the gaugino-mediated SUSY breaking, flavor-violating soft terms arise through the gravity-mediated SUSY breaking which are controlled by the wavefunction localization of the matter superfields. This structure of the model allows us to predict the sparticle mass spectrum including flavor-violating terms. We first explicitly determine the 5D disposition of matter superfields from the low-energy experimental data on SM fermion masses, CKM matrix and the neutrino oscillation parameters. Then, we calculate particle mass spectra and estimate the effects of the flavor-violating soft terms, which should be compared with the current experimental constraints. With gravitino being the lightest sparticle (LSP), the next-to-LSP, which is long-lived, is predicted most likely to be either singlet smuonlike or selectronlike. The model can be tested at collider experiments through flavor-violating processes involving sparticles. The flavor structure among sparticle, once observed, gives us a clue to deep understanding of the origin of Yukawa coupling hierarchy.