The invention discloses a method for quickly identifying differential protein during interaction of chrysanthemum pollen and stigma, belonging to the field of chrysanthemum proteomics. The method comprises the following steps of: performing distant hybridization work of chrysanthemum by taking cultured chrysanthemum as a female parent and wild chrysanthemum as a male parent; cutting off pollinated inflorescences in 1 h and 24 h after pollination; removing petals and sepals of ligulate flowers in the obtained inflorescences to obtain pistils; extracting a protein sample from the obtained pistils by using a TCA (Trichloroacetic Acid)/acetone precipitation method; and quickly identifying the differential protein by applying iTRAQ (Isobaric Tags For Relative And Absolute Quantitation) and a mass spectrum technology and performing bioinformatic analysis. Aiming at the chrysanthemum and wild species of related genera thereof, the invention provides a method for quickly and accurately identifying key differential protein during the interaction of the chrysanthemum pollen and the stigma for providing research foundation for solving the problem of distant hybridization incompatibility of the chrysanthemum.