A distributed control strategy of an energy storage system based on an improved consensus algorithm is proposed to solve the coordinated control problem of multiple energy storage units in an isolated DC microgrid. First, an improved consensus algorithm is proposed, and it is proved that the convergence time of this algorithm is shorter than that of the classical consensus algorithm. Then, based on the improved consensus algorithm, a distributed control strategy for the energy storage system is proposed, one which reasonably adjusts the power of each energy storage unit to maintain the stability of the DC bus voltage and avoid over-charge and over-discharge of energy storage batteries. This strategy has two operational modes applicable to the conditions with and without disturbance respectively. This reduces the amount of communication and computation required for control while adjusting the power of the energy storage unit in a timely fashion. Finally, a simulation example of an isolated DC microgrid system is constructed, and the simulation results verify the effectiveness of the proposed control strategy and its superiority in control time.