We report femtosecond time-resolved measurements of confined acoustic phonons in free-standing nanocrystalline silicon membranes and compare them with the crystalline silicon counterpart. While the latter exhibits well-resolved higher-order modes, a strong suppression of these modes is observed in nanocrystalline samples. The suppression is strongly frequency dependent and becomes more pronounced at shorter phonon wavelengths, consistent with stronger scattering by the nanocrystalline microstructure. Analysis of the phonon lifetimes reveals an additional frequency-dependent scattering mechanism in nanocrystalline silicon, with a scattering rate that scales approximately as $f^2$, where $f$ is the phonon frequency. The measured sound velocity is consistent with previous reports for nanocrystalline silicon and indicates an effective elastic response arising from multiple crystallographic orientations. These results establish coherent phonons as a sensitive probe of microstructure-dependent scattering in nanocrystalline materials and indicate that grain boundaries act as an effective spectral filter for high-frequency acoustic phonons.