The invention relates to a charging-discharging control method and system for energy storage units in a distributed energy storage direct current microgrid. A balance factor is introduced in a controlequation; in a discharging stage, the energy storage unit with the relatively high SOC outputs a relatively high discharging current, and the energy storage unit with the relatively low SOC needs torelease relatively low electricity; and in a charging stage, a charging current of the energy storage unit with the relatively high SOC needs to be maintained at a relatively low level, and the energystorage unit with the relatively low SOC needs to obtain a relatively high charging current, so that the purpose of balancing the SOC of different energy storage units is achieved. The SOC-based balance factor is introduced in an original droop coefficient, so that the charging-discharging conditions of the energy storage units are continuously adjusted along with the SOC values of the energy storage units, the purpose of rapidly balancing the SOC of the energy storage units is achieved, rapid balance of the SOC of the energy storage units can be realized, and the service life of each energystorage unit is prolonged.