A detection element, a manufacturing method thereof and a flat panel detector are disclosed. The detection element includes: a base substrate; a photodiode on the base substrate, the photodiode includes: a first electrode on the base substrate; a photoelectric conversion layer on a side of the first electrode away from the base substrate; 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. Besides, 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; the photoelectric conversion layer includes a sidewall, an orthographic projection of the sidewall of the photoelectric conversion layer on the base substrate is at least partially overlapped with an orthographic projection of the second electrode on the base substrate.