We propose a framework of R-parity violating supersymmetry in a 5D warped space where the Higgs fields live on the IR brane. Quark and lepton multiplets are located in the bulk so that the Yukawa hierarchies arise from their wavefunction profiles. For suppressing dangerous proton decay, we impose a discrete lepton number symmetry on the theory while baryon number conservation is not assumed, which naturally leads to a viable R-parity violation. We assume a supersymmetry breaking sector on the UV brane. Gaugino masses are generated by interactions with the supersymmetry breaking sector or anomaly/radion mediation. Light quark and lepton multiplets couple to the supersymmetry breaking sector and the scalar superpartners are heavy. Light stop masses are generated by gaugino mediation or anomaly/radion mediation. They also receive two-loop corrections from light quarks and leptons when their scalar superpartners are absent in the low-energy theory. We introduce a bulk singlet field localized toward the IR brane to explain the Higgs boson mass and generate the Higgsino mass term at the electroweak scale. The unification of the standard model gauge groups is also discussed. Interestingly, the unified theory emerges just above the IR scale near the TeV scale.