The virtual capacitor control strategy is applied to the converters at each port of DC microgrid to simulate the charge-discharge characteristics of capacitors, which provides an effective solution to solve the inertia problem of the system and improve the voltage quality. Aiming at the cooperative allocation problem of virtual capacitance control in parallel operation of multiple energy storage units, a cooperative allocation strategy of multiple energy storage units based on virtual capacitance control to give full play to the inertial support capability of each energy storage unit is proposed in this paper. The total value of the adjustable virtual capacitance is obtained according to the change rate of DC voltage and the state of charge. The entropy method and scoring matrix are used to comprehensively evaluate the indicators such as the state of charge of the battery and the adjustable capacity of the energy storage converter. The allocation coefficient is obtained according to the final evaluation score, so as to distribute the total virtual capacitance cooperatively. Finally, a hardware-in-the-loop simulation test platform is built to verify the proposed strategy. The results show that the energy storage units allocate virtual capacitors reasonably according to the inertia capacity, which avoids the energy storage converter from prematurely exiting due to excessive output power, and enhances the inertia level and safe and stable operation capability of the system.