The mechanism of self-absorption of Ce:YAP crystals which are grown by Czochralski method is investigated in this paper. Samples with different thickness,concentration and annealing condition are prepared and the corresponding transmittance spectra,photoluminescence and X-ray excited luminescence are measured at room temperature. The mechanism of self-absorption of Ce:YAP crystals is studied and the results show that the self-absorption band peaking at 303 nm is caused by charge transfer transition of Ce4+ ions. The study indicates that the problem of self-absorption can been resolved by effectively minimizing the concentration of Ce4+ions.