We present non-perturbative renormalization factors for $Delta S=2$ four-quark operators in quenched domain-wall QCD using the Schroedinger functional method. Non-perturbative renormalization factor for $B_K$ is evaluated at hadronic scale. Combined
with the non-perturbative RG running obtained by the Alpha collaboration, our result yields renormalization factor which converts lattice bare $B_K$ to the renormalization group invariant one. We apply the renormalization factor to bare $B_K$ previously obtained by the CP-PACS collaboration with the quenched domain-wall QCD(DWQCD). We compare our result with previous ones obtained by perturbative renormalization factors, different renormalization schemes or different quark actions. We also show that chiral symmetry breaking effects in the renormalization factor are numerically small.
