A multi-level switching power converter includes a multi-level power stage circuit which converts an input power to an output power. The power stage circuit includes an inductor, a conversion capacitor and plural power switches. The controller circuit controls the multi-level power stage circuit and includes: a feedback pulse generator circuit which generates a trigger pulse; a first timer circuit and a second timer circuit which determine a first time period and a second time period respectively according to the trigger pulse; and an adjusting circuit which adjusts the first time period according to a difference between the voltage across the conversion capacitor and a reference voltage such that an average of the voltage across the conversion capacitor is substantially equal to a level of the reference voltage.