A fingerprint sensing system including a plurality of micro-lenses, a sensor, a shielding structure and a controller is provided. The micro-lenses are arranged in an array. The sensor has a plurality of sensing pixels arranged in an array. The sensor, the shielding structure and the micro-lenses are sequentially arranged along an arrangement direction. The controller is electrically connected to the sensor. A pitch between the micro-lenses is greater than a pitch between the sensing pixels. The controller forms a fingerprint image according to signals of a plurality of output pixels of the sensor, wherein each of the output pixels is one of every at least four of neighboring sensing pixels. An operation method of a fingerprint sensing system is also provided.