A LED illumination system with multiple independent loops includes an input unit provided to receive a D.C. voltage, and a plurality of light module control circuits electrically connected to the input unit. Each of the light module control circuits includes a light module controller and two filtering units. The two filtering units are electrically connected to the light module controller, and receive D.C. power transmitted form the input unit to drive two set of LED illuminators, respectively. The light module controller controls current of the two set of LED illuminators via the two filtering units so as to control brightness of the LED illuminators, respectively. Therefore, the LED illuminators are controlled by the independent loops to reduce mutual influence among the LED illuminators.