An auxiliary battery recharging control method and apparatus are provided. The method includes determining whether a recharging prohibition condition is established, based on first state information of a vehicle and second state information of a first battery, at regular recharging intervals, when a periodic recharging mode is executed, based on a first ignition (IG) voltage. Recharging is executed based on whether a critical recharging condition is established using third state information of a second battery, when an automatic recharging mode is executed, based on a second IG voltage. Additionally, a voltage variation is calculated of the second battery selected from the third state information, and at least one of a recharging time and a recharging voltage is adjusted, based on the calculated voltage variation, or the recharging interval is adjusted, based on the calculated voltage variation.