The inter- and intramolecular hydrogen-bonding modes of two steric isomers, namely fumaric acid and maleic acid, are observed by using terahertz time-domain spectroscopy (THz-TDS). The intermolecular modes observed with fumaric acid crystals are inactivated by incorporating the molecules in the nano-sized pores of a mesoporous silicate (SBA-16) due to the separation of the molecules, whereas the intramolecular modes of maleic acid of the crystal and the incorporated samples are similar.