Superconductivity mediated by phonons is typically conventional, exhibiting a momentum-independent s-wave pairing function, due to the isotropic interactions between electrons and phonons along different crystalline directions. Here, by performing inelastic neutron scattering measurements on a superconducting single crystal of Sr_0.1Bi₂Se₃, a prime candidate for realizing topological superconductivity by doping the topological insulator Bi₂Se₃, we find that there exist highly anisotropic phonons, with the linewidths of the acoustic phonons increasing substantially at long wavelengths, but only for those along the [001] direction. This observation indicates a large and singular electron-phonon coupling at small momenta, which we propose to give rise to the exotic p-wave nematic superconducting pairing in the M_xBi₂Se₃ (M = Cu, Sr, Nb) superconductor family. Therefore, we show these superconductors to be example systems where electron-phonon interaction can induce more exotic superconducting pairing than the s-wave, consistent with the topological superconductivity.