The invention provides a cold-tolerance gene qCT-3-2HHZ for rice booting stage stable expression and a molecular marking method thereof, and belongs to the field of rice high-yield stress-tolerance breeding and molecular genetics. According to the linkage and linkage disequilibrium phenomenon, the Huang zhanhua variety and eight associated breeding populations derived from donor parents rich in diversity are used, a whole-genome relational analysis and physical mapping method is adopted, the cold-tolerance gene qCT-3-2HHZ for the rice booting stage stability expression is precisely positioned and verified, and a practical economical marker ZCT-7 based on common PCR is further developed. The cold-tolerance gene qCT-3-2HHZ and the molecular marking method are applied to rice chilling-injury-tolerance assisted selection and pyramid breeding, defects of natural variation genes in the prior art can be effectively made up for, negative effects caused by assistant breeding conducted through primary positioning results can be remarkably reduced, genotype selection can be carried out on low-generation breeding populations in the seedling stage, cold-tolerance individuals are obtained, hybridization and transfer are facilitated in time, the process of identifying low-temperature resistance in the adult-plant stage is omitted, breeding efficiency is improved, and the breeding process is accelerated.