A control system of a low voltage DC-DC converter is provided. The system includes a low voltage DC-DC converter unit that has a power semiconductor element and converts power supplied from a high voltage battery of a vehicle into power of low voltage. A switching frequency change unit changes a switching frequency of the power semiconductor element and a microcomputer generates a final PWM signal based on an input voltage value input from the high voltage battery and an output voltage value of the switching frequency change unit to apply a maximum duty command voltage to a PWM controller. The PWM controller applies PWM voltage to the power semiconductor element to thus operate the power semiconductor element at less than a maximum duty based on the maximum duty command voltage applied from the microcomputer.