The invention provides an antigen epitope polypeptide CD44-P3 based on a prostate cancer stem cell marker CD44 and application thereof, and relates to the technical field of biological medicine engineering. According to the antigen epitope polypeptide CD44-P3 based on the prostate cancer stem cell marker CD44 and the application thereof provided by the invention, an antigen epitope polypeptide isdesigned and synthesized by adopting bioinformatics means on basis of the prostate cancer stem cell surface-marker CD44. The synthesized antigen epitope polypeptide is capable of specifically activating cytotoxic T lymphocytes, and has good killing effect; and thus, the antigen epitope polypeptide can be used for developing therapeutic peptide vaccines targeting prostate cancer stem cells, therebyproviding new technical schemes for precise immunotherapy of malignant prostate cancer. In addition, specific targeting on prostate cancer stem cells is also enabled so as to fundamentally reduce recurrence of prostate cancer.