This paper proposes an inertia-emulation-based cooperative control strategy for the multi-parallel energy storage system (ESS) to meet the requirements of state-of-charge (SoC) balance, inertia enhancement and zero-steady-state voltage deviation. The inertia emulation loop (IEL) is constructed by analogy with DC motors to dampen voltage oscillation, while the secondary voltage recovery loop is derived from the circuit equivalence of an inductor to indicate the system stiffness. Moreover, to equalize SoCs of energy storage units (ESUs) dynamically, a SoC self-balance algorithm is developed. The redefined SoC mismatch degree and balance speed adjustment factor k are introduced into the droop resistance, adjusting the SoC self-balance rate and eliminating the SoC deviation among ESUs. The dynamic performance of the SoC self-balance algorithm is analyzed and the small signal model of the DC microgrid (DC-MG) with proposed strategy is established. Based on eigenvalue analysis and step response, the system stability is assessed, and the influence of control parameters on transient characteristics and stability margin is investigated. Considering power constraint, voltage deviation constraint and dynamic stability constraint, the optimal design method of k is given. Finally, simulation and experiment verify that the proposed control, without modifying hardware, performs better dynamic and static characteristics and can equalize SoC among ESUs in charge and discharge mode.