The invention provides a goat milk proteome comparing method. The method includes the steps of a, collecting milk samples; b, preparing a solution; c, preparing skim milk protein samples; d, measuring the concentration of the sample protein, to be more specific, using a BCA kit, allowing PBS to be blank, using 5.0mg / mL BSA as the standard protein, and measuring the OD value of the sample protein with a microplate reader under the wavelength of 560 nanometers to obtain the protein concentration of the colostrum skim milk protein sample and the normal skim milk protein sample; e, performing two-dimensional gel electrophoresis, to be more specific, sequentially performing isoelectric focusing electrophoresis, gel strip equilibrium, SDS-PAGE vertical gel electrophoresis and gel image collecting and analysis to obtain the 2-DE spectrum of the colostrum milk sample and the normal milk sample. The goat milk proteome comparing method has the advantages that the protein components of biological systems can be analyzed in a large-scale manner at the same time, and a theoretical basis is provided for the systematic disclosing of the change law of goat milk proteome along with lactation stages.