A multi-output control system includes a power conversion module, a first active linear module, a second active linear module, a control module and a feedback control module. The control module controls the feedback control module to adjust an output power based on current signals. The first active linear module and the second active linear module determine whether a difference value between a current value of a first output power and a current value of a second output power is greater than a current difference predetermined value based on the current signals, and the control module adjusts a voltage value of the first output power and a voltage value of the second output power to respectively be within a predetermined voltage range based on the current signals.