  We propose a novel mechanism for reproducing the realistic hierarchical
structure of the observed CKM mixing matrix and quark masses by means of
introducing a warped metric. We illustrate the method on the basis of a
specific Type IIA intersecting brane model proposed by Ibanez et al. The model
is compactified on a direct product of three tori, on which four D-brane stacks
wrap, and the intersections between two stacks collectively provide three
generations of quarks and leptons. The exponential of the area formed by the
intersection points corresponding to three matter fields is interpreted as the
Yukawa coupling among them. It is known, however, that the Yukawa matrices for
quarks are generically singular, and that it does not give definite mixing
angles nor hierarchically suppressed quark masses. We show that the newly
introduced warp effect on the internal manifold modifies the Yukawa matrix
elements and generate hierarchical quark masses and CKM mixing angles.
