The coupling of plasmonic resonances with the multiple phonon modes of a plasmonic supracrystal is studied. Ultrafast optical pump-probe spectroscopy with variable wavelength allows the selective detection of the breathing mode, the interparticle vibrations, and the vibration of the whole structure. Thanks to this selectivity, the characterization of the bonding strength between nanoparticles in different directions of the supracrystal is possible. The observation of these vibrations could be useful for the realization of future phonon modulated photonic and plasmonic devices.