The electron-doped SrTiO3 exhibits good thermoelectric properties, which makes this material a promising candidate of an n-type oxide thermoelectric device. Recent studies indicated that only a few percent co-doping of La and Mn in SrTiO3 substantially reduces the thermal conductivity, thereby greatly improving the thermoelectric figure of merit at room temperature. Our time-of-flight neutron scattering studies revealed that by doping both La and Mn into SrTiO3, the inelastic scattering spectrum shows a momentum-independent increase in the low-energy spectral weight approximately below 10 meV. The increase in the low-energy spectral weight exhibits a clear correlation with thermal conductivity. The correlation is attributed to dynamical and local structural fluctuations caused by the Jahn-Teller instability in Mn3+ ions coupled with the incipient ferroelectric nature of SrTiO3, as the origin of the low thermal conductivity.