With an objective to actively decouple the power flow of the output bridges of a Triple Active Bridge (TAB) converter topology, a novel control strategy is proposed in this paper. Closed form equations of power flow between the three bridges are obtained by modelling and characterizing the TAB structure as a three-port transmission network connected via line inductances using fundamental harmonic approximation (FHA). Various control parameters such as full-bridge duty ratios and phase-shift angles along with their effect of the port voltages and the power flows are explained in depth, that portray the interdependency of the power flows between the three ports. With the correlation obtained between the power flows and the control parameters, a Multi-Input-Multi-Output (MIMO) based control strategy is introduced that regulates the power flow for both the output side bridges independently. This is achieved by including cross-gain terms in the conventional control scheme that actively cancels out the coupling effect between the control loops. Further, to elucidate the effectiveness of the proposed control scheme, detailed simulation analyses have been presented. The results describe that due to the decoupled control scheme, the secondary side output voltage stays constant with a maximum variation of ±4%, for a sudden load reduction in the tertiary bridge. In addition to that, a 300W laboratory prototype is developed to observe the performance of the proposed control scheme and the results portray strong coherence with the simulation results, along with an end-to-end efficiency of 94.4%.