In this work, we perform nonequilibrium molecular dynamics simulations to study phonon scattering at two tilt grain boundaries (GBs) in SrTiO3. Mode-wise energy transmission coefficients are obtained based on phonon wave-packet dynamics simulations. The Kapitza conductance is then quantified using a lattice dynamics approach. The obtained results of the Kapitza conductance of both GBs compare well with those obtained by the direct method, except for the temperature dependence. Contrary to common belief, the results of this work show that the optical modes in SrTiO3 contribute significantly to phonon thermal transport, accounting for over 50% of the Kapitza conductance. To understand the effect of the GB structural disorder on phonon transport, we compare the local phonon density of states of the atoms in the GB region with that in the single crystalline grain region. Our results show that the excess vibrational modes introduced by the structural disorder do not have a significant effect on phonon scattering at the GBs, but the absence of certain modes in the GB region appears to be responsible for phonon reflections at GBs. This work has also demonstrated phonon mode conversion and simultaneous generation of new modes. Some of the new modes have the same frequency as the initial wave packet, while some have the same wave vector but lower frequencies.