The printing quality delivered by a drop-on-demand inkjet printhead is severely affected by the residual oscillations in an ink channel and the cross-talk between neighboring ink channels. For a single ink channel, our earlier contribution shows that the actuation pulse can be designed, using a physical model, to effectively damp the residual oscillations. It is not always possible to obtain a good physical model for a single ink channel. A physical model for a multi-input multi-output (MIMO) inkjet printhead is made even more sophisticated by the presence of the cross-talk effect. This paper proposes a system identification-based approach to build a MIMO model for an inkjet printhead. Additionally, the identified MIMO model is used to design new actuation pulses to effectively minimize the residual oscillations and the cross-talk. Using simulation and experimental results, we demonstrate the efficacy of the proposed method.