Although the thermoelectric figure of merit zT above 300 K has seen significant improvement recently, the progress at lower temperatures has been slow, mainly limited by the relatively low Seebeck coefficient and high thermal conductivity. Here we report, for the first time to our knowledge, success in first-principles computation of the phonon drag effect--a coupling phenomenon between electrons and nonequilibrium phonons--in heavily doped region and its optimization to enhance the Seebeck coefficient while reducing the phonon thermal conductivity by nanostructuring. Our simulation quantitatively identifies the major phonons contributing to the phonon drag, which are spectrally distinct from those carrying heat, and further reveals that although the phonon drag is reduced in heavily doped samples, a significant contribution to Seebeck coefficient still exists. An ideal phonon filter is proposed to enhance zT of silicon at room temperature by a factor of 20 to ∼ 0.25, and the enhancement can reach 70 times at 100 K. This work opens up a new venue toward better thermoelectrics by harnessing nonequilibrium phonons.