The invention provides a fingerprint sensing circuit and a control method thereof. The fingerprint sensing circuit includes a fingerprint detection capacitor having one end coupled to a finger; a detection electrode coupled to the fingerprint detection capacitor; a driving voltage interface adapted to alternately load the driving voltages of the high and low levels to the detection electrode; an amplifier; a first switch adapted to selectively couple the detection electrode to the inverting input end of the amplifier; a reference voltage interface adapted to alternately input the reference voltages of the high and low levels to the normal-phase input end of the amplifier; a control unit adapted to generate a control signal such that the amplifier outputs a first output voltage and a second output voltage after a time sequence period is completed; and a subtraction circuit adapted to use the difference value between the first output voltage and the second output voltage as an output signal of the fingerprint sensing circuit. The fingerprint sensing circuit reduces the low-frequency common-mode noise signal and improves the output voltage signal to noise ratio and fingerprint sensitivity.