Manipulating lattice vibrations is the cornerstone to achieving ultralow thermal conductivity in thermoelectrics. Although spatial control by novel material designs has been recently reported, temporal manipulation, which can shape thermoelectric properties under nonequilibrium conditions, remains largely unexplored. Here, taking SnSe as a representative, we have demonstrated that in the ultrafast pump-pump-probe spectroscopy, electronic and lattice coherences inherited from optical excitations can be exploited independently to manipulate phonon oscillations in a highly selective manner. Specifically, when the pump-pump delay time (tmod) is in the electronic coherence time range, the amplitude, frequency, and lifetime of all phonon modes are simultaneously following the optical cycle. While extending tmod into the lattice coherence time range, the amplitude of each coherent phonon mode can be selectively manipulated according to its intrinsic period without changing the frequency and lifetime. This work opens up exciting avenues to temporally and discriminatorily manipulate phononic processes in thermoelectric materials.