The technical problems caused by load fluctuation in the power system of electric propulsion research ship during the research operation are analyzed, the solution of adding the lithium iron phosphate energy storage unit into the power system is proposed, so as to make the power system run more stable with the peak clipping and valley filling capability of energy storage unit. At the same time, taken the intelligent unmanned system carrier as an example, the key technology of zero emission that the energy storage system combined with power battery system realizes the pure electric propulsion when the ship enters and leaves the port is introduced. The configuration scheme and charge and discharge scheduling control mode of electric propulsion distribution system containing the lithium iron phosphate energy storage unit are proposed, which can provide solutions and reference for engineers to design the similar research ships.