The invention discloses a screening method of mildewed seeds, and belongs to the field of seed selection. A device comprises an ultraviolet fluorescent tube, a visible light single-color CCD (charge coupled device) sensor, a two-dimension grabbing mechanism, a single-layer seed conveying device and a control system, wherein the ultraviolet fluorescent tube, the visible light single-color CCD sensor, the two-dimension grabbing mechanism and the single-layer seed conveying device are electrically connected with the control system respectively. The autofluorescence characteristic of fungi is used, that is, to-be-processed seeds are irradiated by 356 nm ultraviolet rays, and the mildewed seeds are identified by detecting fluorescence excitation of the mildewed seeds under radiation of 356 nm ultraviolet rays. The method has the characteristics that the cost is low, industrialized screening of the mildewed seed is realized, and the demand of seed engineering for automatic production is met; the screening efficiency and the accuracy are higher, seed processing by an organic solvent and the like is reduced, and damage to healthy seeds is reduced, growth of the seeds cannot be influenced, environmental pollution is reduced, the cost is reduced and the like.