We report the synthesis of new coupling agents with internal amide or urea groups possessing an epoxy-terminal group and trimethoxysilyl-anchoring group. The structural characterizations of the corresponding self-assembled monolayers (SAMs) were performed by polarization modulation infrared reflection adsorption spectroscopy (PM-IRRAS). The molecular assembly is mainly based on the intermolecular hydrogen-bonding between adjacent amide or urea groups in the monolayers. Because of the steric hindrance of amide or urea groups, the distance between the alkyl chains is too large to establish van der Waals interactions, inducing their disorder. The reactivity of the epoxy-terminal groups was successfully investigated through reaction with a fluorescent probe. We show that SAMs containing internal urea or amide groups exhibited a higher density of accessible epoxide groups than the corresponding long-chain (C22) glycidyl-terminated SAM.