We study the branching ratios, the direct CP asymmetries in B→K(*)K̄(*) decays and the polarization fractions of B→K*K̄* decays by employing the QCD factorization in the minimal supersymmetric standard model with R-parity violation. We derive the new upper bounds on the relevant R-parity violating couplings from the latest experimental data of B→K(*)K̄(*), and some of these constraints are stronger than the existing bounds. Using the constrained parameter spaces, we predict the R-parity violating effects on the other quantities in B→K(*)...