Protonated titanate nanotubes (TiNT-H) were surface-modified with (3-aminopropyl)trimethoxy silane (APTMS) by a novel method suitable for the syntheses of large amounts of materials at a low cost. The usage of prepared nanotubes for polymer reinforcement was studied. Since the thermal stability of the nanofiller was important to preserve its functional properties, its stability was studied by in situ high-temperature measurements. The most thermally stable nanotubes were silanized for 20 min and used for the preparation of epoxy-based nanocomposites. The nanofiller formed smaller (a few hundred nm) and larger (a few μm) aggregates in the polymer matrix, and the amount of aggregates increased as the nanofiller content increased. The APTMS-modified titanate nanotubes bonded well with the epoxy matrix since amine groups on the TiNT's surface can react with an epoxy group to form covalent bonds between the matrix and the nanofiller. A very small addition (0.19-1.52 wt%) of the nanotubes significantly increased the glass transition temperature and the modulus in the rubbery state of the epoxy-based polymer. Smaller nanofiller content leads to a larger increase in these parameters and therefore better dynamic mechanical properties due to the smaller amount of large aggregates. APTMS-modified titanate nanotubes have proven to be a promising nanofiller in epoxy-based nanocomposites.