We propose a method to investigate the vibrational dynamics of single polyatomic molecular ions confined in a Paul trap. Quantum logic techniques are employed to detect the recoil of single photon absorption events on the molecule via a co-trapped atomic ion. In particular, the recoil is mapped onto the electronic state of the atom which can be read out with high fidelity. This recoil detection serves as the basis for a pump-probe scheme to investigate ultrafast molecular dynamics, such as intra-molecular vibrational redistribution. The total recoil from the interaction with a sequence of ultrafast laser pulses with the molecular vibration is measured. This work discusses the experimental requirements and expected performance for multiple molecular ions with masses ranging from 17 to 165 Dalton.