A flat panel detector and an imaging system are provided. The flat panel detector includes a plurality of pixel units which include photosensitive pixel units and alignment pixel units. Each photosensitive pixel unit includes a photoelectric sensor configured to convert an incident light into an electrical signal so that a photosensitive pixel unit in which the photoelectric sensor is located has a grayscale that changes according to a real-time change of the incident light. Each alignment pixel unit is configured to have a fixed grayscale, and the fixed grayscale does not change according to the real-time change of the incident light. The alignment pixel units includes first alignment pixel units and second alignment pixel units. Each first alignment pixel unit has a first fixed grayscale, each second alignment pixel unit has a second fixed grayscale different from the first fixed grayscale.