A battery charging control system for a vehicle includes: a high voltage battery supplying power to a driver of the vehicle; an auxiliary battery supplying power to an electric load of the vehicle; a first voltage converter connecting between the high voltage battery and the auxiliary battery; a second voltage converter connecting between the high voltage battery and the electric load; a switch having one side connected to a circuit line between the first voltage converter and the auxiliary battery and the other side connected to a circuit line between the second voltage converter and the electric load; and a controller controlling a turn on/off of the first voltage converter and the second voltage converter and a turn on/off of the switch depending on whether the first voltage converter and the second voltage converter is broken and the auxiliary battery needs to be charged.