A cross regulation controller and the methods for controlling a boost converter are proposed. The boost converter includes the first and second switch elements, and the first and second output capacitors. The cross regulation controller includes a first feedback control circuit for processing the second voltage, a sampling of the voltage across the second output capacitor, with a reference voltage to produce a third voltage and to transform the third voltage to generate a first pulse signal to drive the first switch element, and a second feedback control circuit for processing the first voltage, a sampling of the voltage across the first output capacitor, with a reference voltage to produce a fourth voltage and to transform the fourth voltage to generate a second pulse signal to drive the second switch element so as to achieve a balancing status between the first voltage and the second voltage.