The invention discloses a method for identifying embryo abortion associated proteins of distant hybridization of chrysanthemum, and belongs to the field of chrysanthemum breeding and proteomics. The method comprises the steps of planting the small chrysanthemum as a female parent, taking wild chrysanthemum nankingense as a male parent for distant hybridization, cutting off pollinated inflorescences at different times after pollination, sampling ovaries with complete and plump morphological development and ovaries with abnormal and hollow morphological development respectively, immediately quick-freezing in liquid nitrogen after sampling, storing in a refrigerator at -80 DEG C, extracting proteins from samples by a TCA (Trichloroacetic Acid)/acetone precipitation method, quickly identifying differential proteins by an iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) and mass-spectrometric technique, performing bioinformatic analysis, and obtaining the embryo abortion associated protein in the distant hybridization breeding of the chrysanthemum. The method can quickly and accurately identify the embryo differential proteins with different morphologies in different developmental stages during embryonic development of the chrysanthemum for the chrysanthemum and affinis wild species of the chrysanthemum, and a research foundation is provided for solving embryo abortion of the distant hybridization of the chrysanthemum.