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Introduction Peanut cultivation in high-latitude regions is frequently subjected to low-temperature stress, which adversely affects peanut growth and development. The correlation between physiological changes in peanut during the germination and seedling stages and exposure to low-temperature stress at the harvest period remains unclear, and this research gap limits the in-depth study of peanut cold tolerance. This study aimed to explore the above correlation and identify core physiological indicators for evaluating peanut cold tolerance at germination and seedling stages. Methods Thirty-six peanut accessions were used as experimental materials and subjected to natural low-temperature stress during the field harvest period. After drying the pods for 3 days, laboratory germination tests were conducted to screen out one extremely cold-tolerant and one extremely cold-sensitive accession from the 36 materials. The two extreme materials were then exposed to artificial low-temperature stress at the germination and seedling stages: the temperature was decreased from 26 °C to target temperatures (8 °C, 4 °C, and 0 °C) at a rate of 2 °C/h, and then increased back to 26 °C at the same rate, with a control group maintained at a constant 26 °C. Physiological indicators of the materials were determined at five time points after they returned to 26 °C and resumed normal growth, and principal component analysis (PCA) was used for comprehensive analysis of the indicators. Results After low-temperature stress at both germination and seedling stages, the cold-tolerant material had significantly higher contents of proline (Pro) and soluble sugar, as well as higher activities of Superoxide Dismutase (SOD), Peroxidase (POD), and Catalase (CAT) compared with the cold-sensitive material, while its Malondialdehyde (MDA) content was significantly lower. All physiological indicators of the cold-tolerant material recovered to normal levels within 36 hours of recovery, whereas the recovery of the cold-sensitive material was significantly slower. PCA extracted three principal components from the measured indicators, with a cumulative contribution rate of 89.35%. Pro and SOD were ultimately identified as the core indicators for evaluating peanut cold tolerance at the germination and seedling stages. Discussion This study successfully screened two peanut materials with extreme cold tolerance phenotypes by combining field natural low-temperature stress and laboratory simulated low-temperature stress treatments. The clarification of Pro and SOD as core evaluation indicators fills the research gap in the cross-stage cold tolerance study of peanuts, which links harvest-period low-temperature stress with physiological responses at germination and seedling stages. The screened extreme cold-tolerant and cold-sensitive materials provide important germplasm resources for subsequent peanut cold tolerance breeding, and the identified core indicators lay a solid theoretical foundation for the rapid evaluation and identification of peanut cold tolerance.