We have developed microporous organic–inorganic hybrid nanocomposites by alkoxysilylation of 4,4′-biphenyl-bridged alkoxysilane compounds, which contain triethoxysilyl, methyldiethoxysilyl, and dimethylethoxysilyl groups at each end of the 4,4′-biphenylene unit ((CH3)n(C2H5O)3−n-Si-C12H8-Si-(OC2H5)3−n(CH3)n, n = 0, 1, or 2, abbreviated as BESB(0), BESB(2), or BESB(4), respectively, where the number in parentheses indicates the number of methyl groups in these molecules), in the interlayer of a crystalline layered silicate, ilerite. XRD, 29Si solid-state NMR and fluorescence spectroscopy revealed the immobilization and bridging formation of the BESB molecules between the silicate layers by condensation, not only with H-ilerite, but also with the BESB molecules. The interlayer structures exhibited different molecular arrangements. BESB(0) and BESB(4) molecules are present as a monolayer arrangement in which BESB(0) molecules form the oligomeric species caused by close stacking like a dimer. BESB(2) molecules form mainly bilayer-like aggregates in the interlayer. The structural differences are caused by the different reactivities of the BESB molecules, which control their polymerization in the interlayer. The resultant BESB(0)- and BESB(2)-ilerite had high microporosity with BET surface areas (508 and 578 m2 g−1 for BESB(0)- and BESB(2)-ilerite, respectively). The micropores showed higher toluene adsorptivity than several other porous silica materials due to the successful surface modification. Consequently, this approach provides a new method for constructing novel microporous nanocomposites, the key to improved selectivity and activity in separation and catalytic applications.