A flat panel detector and a manufacturing method thereof. The flat panel detector includes a first substrate and a second substrate. The first substrate includes a driving circuit, the second substrate includes a photosensitive element, the first substrate and the second substrate are arranged opposite to each other so as to be assembled, and the driving circuit is electrically connected with the photosensitive element to drive the photosensitive element. The flat panel detector not only can improve the filling rate of a photodiode in a pixel unit and increase the photosensitive area of the pixel unit in the flat panel detector, but also can effectively prevent static electricity and scratches generated during use and improve the photoelectric characteristics and yield of the flat panel detector.