The invention provides a rapid and stable animal individual genome breeding value evaluation method, and relates to the technical field of animal breeding. The rapid and stable animal individual genome breeding value evaluation method comprises the steps that an HIBLUP is adopted and utilizes phenotype information, genotype information and spectrum information to predict genome breeding values, and the final output genome breeding values comprise estimated individual genetic value, additive and dominant effect values of each individual, and a reverse analytic value of each genetic marker effect in a genotyping chip. According to the rapid and stable animal individual genome breeding value evaluation method, the spectrum information, the phenotype information and the genotype information are fully utilized to predict the genetic value (the additive and dominant effects) of each animal and the effective value of each SNP marker site, the most advanced genome breeding value prediction andvariance component estimation algorithm is achieved, and thus genome selection is achieved.