3-aminopropyltriethoxysilane (APTES) was used as a coupling agent to graft thermoplastic polyurethane (TPU) onto a nanosilica surface. The modification of TPU on the surface of silica nanoparticles was confirmed by FTIR, NMR, ESCA and TGA assessment. The grafting degree of TPU onto the silica was about 7.3%. The incorporation of surface-modified silica (TAS50) into poly(lactic acid) (PLA) induced the nucleation of PLA, giving a higher crystallisation peak temperature, which would be advantageous for fast processing cycles in the commercial moulding process. With pristine silica incorporated into PLA, the variation in the cold crystallisation and melting temperatures was limited. However, for the surface-modified silica filled PLA, a lower cold crystallisation temperature at 112.1 °C and a shift of melting temperature from Tm1 to Tm2 at 167.7 °C were observed. The cooling rate also played an essential role in the derived crystalline forms. The tensile strength of the composite containing modified silica was slightly higher than that with the pristine silica, even though both showed similar degrees of silica dispersion from the morphology observation. For the surface-modified silica composite, the optical transmittance was higher than that of unmodified silica case. This finding implies the significance of the surface modification.