A supplementary charging system for an auxiliary battery of an eco-friendly vehicle includes: a main battery; an auxiliary battery having a voltage lower than a voltage of the main battery; a low voltage DC-DC converter (LDC) stepping down the voltage of the main battery and providing the stepped-down voltage to the auxiliary battery; and a controller configured to select, when a periodic charge time of the auxiliary battery arrives, either a constant voltage charging method or a constant current charging method as a charging method based on an aging state of the auxiliary battery, and control the LDC to charge the auxiliary battery with a constant voltage or a constant current based on the selected charging method for a predetermined reference time. The controller terminates the charging when a cumulative charge current amount is greater than or equal to a predetermined reference cumulative charge current amount.