The present work investigated the alleviation of chilling injury in response to exogenous polyamines in “Eureka” lemon (Citrus limon) fruits stored at low temperature. The lemon fruits were immersed either in polyamine solutions [1 mmol/L putrescine (PUT), 1 mmol/L spermidine (SPD), or 0.5 mmol/L PUT + 0.5 mmol/L SPD (combined)] or in distilled water (control). The morphology, cellular structure (using transmission electron microscopy), chilling injury (CI) index, total soluble solids (TSS), titratable acid (TA), malondialdehyde contents, and membrane permeability, as well as the peroxidase (POD) and polyphenol oxidase (PPO) activities of the lemon fruits were measured after 0, 15, 30, and 45 days of storage at -2 ± 0.5°C. Results showed that lemon fruits treated with polyamine had higher amounts of TSS and TA, as well as POD and PPO activities. The PUT, SPD, and combined treatments exhibited significantly reduced electrolyte leakage and less evidence of chilling injury. This indicated that the synergistic effects of PUT and SPD protected the fruit from chilling injury and maintained the postharvest quality of the lemon fruits better than PUT or SPD alone did.