Control of nanostructure formation by a diblock-type supramacromolecule via biocomplementary hydrogen bonding has been achieved. Two different homopolymers, poly(4-trimethylsilylstyrene) and poly(styrene-d8), that are end-decorated with complementary oligonucleotides, i.e., thymidine phosphates and deoxyadenosine phosphates, were prepared by using the phosphoramidite method and blended successively. Association behavior in a blend solution was examined with NMR, and a cast bulk film obtained from the solution has been confirmed to show a nanophase-separated structure by transmission electron microscopy and X-ray scattering. Suppression of this nanostructure formation of a block-type supramacromolecule was also attained by adding a smaller agent as an inhibitor.