The interaction of individual electrons with vibrations has been extensively studied. However, the nature of electron-vibration interaction in the presence of many-body electron correlations such as a Kondo state has not been fully investigated. Here, we present transport measurements on a Copper-phthalocyanine molecule, suspended between two silver electrodes in a break-junction setup. Our measurements reveal both zero bias and satellite conductance peaks, which are identified as Kondo resonances with a similar Kondo temperature. The relation of the satellite peaks to electron-vibration interaction is corroborated using several independent spectroscopic indications, as well as ab initio calculations. Further analysis reveals that the contribution of vibration-induced inelastic current is significant in the presence of a Kondo resonance.