The invention discloses a high-
throughput method for segregating a quantitative character regulatory 
gene, which comprises the following steps of: 1) construction of a target character segregation 
population, in which the 
population is a 
population in two parent hybridization progenies (F2 and F3), a DH 
system and a RIL; 2) mixing of extreme samples and segregation of 
total RNA in the population, in which a progeny segregation population is divided into three categories according to character 
phenotype; 3) 
gene expression analysis, in which the difference and sameness of 
gene expressions between two extreme mixed samples are compared by utilizing a 
gene expression analysis method, namely one of 
chip, EST sequencing, subtraction, cDNA-AFLP, and the like; and 4) acquisition and 
verification of a 
candidate gene, in which a 
differential expression gene between the two extreme mixed samples is found and is a candidate regulatory gene related to target character, and the function of the gene is verified through 
transgene, 
gene expression, 
molecular marker correlation and a contribution 
rate analysis method to obtain a 
target gene with regulatory character 
phenotype. The method is suitable for the segregation of a certain quantitative character regulatory gene controlled by multigene of all organisms, and is a simple, quick, high-
throughput and economical gene segregation method.