The present invention provides a capacitance determining circuit comprising a touched layer configured to receive a touch from a finger; a shielding layer disposed under the touched layer, wherein a parasitic capacitance is formed between the shielding layer and the touched layer; a driving circuit coupled to the touched layer and the shielding layer, configured to provide a first voltage to the touched layer and the shielding layer at a first time; a sensing circuit electrically connected to the touched layer, configured to sense the touch capacitance at a second time; and a first switch with a terminal electrically connected to the shielding layer and another terminal electrically connected to the driving circuit or the touched layer. The capacitance determining circuit and the fingerprint recognition system provided by the present invention is capable of eliminating parasitic capacitance effect and enhancing accuracy and performance of capacitance sensing and fingerprint recognition.