A fingerprint sensing system is configured to receive an illumination beam which is reflected by a finger and then transmitted to the fingerprint sensing system to generate a fingerprint image. The fingerprint sensing system includes a plurality of microlenses, a sensor, a first light filter layer, and a second light filter layer. The microlenses are arranged in an array. The sensor has a plurality of sensing pixels arranged in an array. The first light filter layer is disposed between the microlenses and the sensor and has a plurality of first openings. The second light filter layer is disposed between the first light filter layer and the sensor and has a plurality of second openings. The illumination beam passes through the first openings or the second openings, so that the sensor receives the illumination beam.