This paper proposes a novel robust trajectory tracking controller for multi-mass resonant systems, i.e., flexible mechanical systems, by using Differential Flatness (DF) and Disturbance Observer (DOb) in state space. The former regulates the nominal performance of the trajectory tracking control when all disturbances are neglected; e.g., the vibration at tip is simply suppressed by placing all nominal poles on the real axis via a state feed-back controller. However, it is sensitive to plant uncertainties and external disturbances so the nominal performance may significantly change in real implementations. The latter is used to improve the robustness; i.e., the nominal performance can be achieved by suppressing disturbances in practice when DOb is implemented. The states of the system are reconstructed by using the estimations of disturbances and their successive derivatives so that the mismatched disturbances are automatically cancelled by their estimations. The matched disturbances are cancelled by directly feeding-back their estimations through control input. Consequently, a simple yet efficient robust trajectory tracking controller is designed for multi-mass resonant systems in state space. It can precisely follow reference trajectories without requiring the exact dynamic model of the system in real implementations. Experimental results are given to validate the proposal.