The invention provides a fluorescent marker rice seed sorting mechanism and method. The fluorescent marker rice seed sorting mechanism comprises a blanking mechanism (1), a profiling positioning mechanism (2), a conveying mechanism (3), a detection device (4), an injection mechanism (5), a collecting channel (6), a light source (7) and a frame (8), wherein the frame (8 )comprises a support frame (81), an upper positioning plate (82), a middle positioning plate (83) and a side positioning plate (84), the detection device (4) and the injection mechanism (5) in the conveying mechanism (3) are correspondingly provided with a detection station and an injection station, the collecting channel (6) is aligned with the injection station, and the light source (7) is aligned with the detection station. The fluorescent marker rice seed sorting mechanism is simple and compact in structure, convenient to use and capable of stably, uniformly and orderly loading and transporting the seeds, the detection area is wide, multiple times of detection can be carried out, and the precision of seed sorting is greatly improved.