A detection element, a manufacturing method thereof and a flat panel detector are disclosed. The detection element includes: a base substrate; a first electrode on the base substrate; a photoelectric conversion layer; a transparent electrode and a second electrode electrically connected with the transparent electrode on a side of the photoelectric conversion layer away from the first electrode. An orthographic projection of the photoelectric conversion layer on the base substrate completely falls within an orthographic projection of the first electrode on the base substrate, in a plane parallel to the base substrate, the transparent electrode is located at a middle portion of the photoelectric conversion, an orthographic projection of a portion of the photoelectric conversion layer not covered by the transparent electrode on the base substrate at least partially falls within an orthographic projection of the second electrode on the base substrate.