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Seed longevity is crucial for long-term storage, but prolonged unfavorable conditions can lead to loss of viability. This study integrated theoretical and experimental techniques to elucidate the inherent mechanisms underlying the unique ability of lotus seeds to maintain stable viability over many years. Transcriptome analysis and microscopy revealed a sturdy structure of the lotus seed pericarp, which predominantly expressed cellulose synthase genes involved in cell wall biogenesis. The cotyledon serves as a nutrient source for seeds during long-term storage. Additionally, the inactivation of chlorophyll degradation pathways may allow for the retention of chlorophyll in the lotus seed plumule, potentially enhancing the environmental adaptability of lotus seedlings. Reduced abundance of transcripts corresponding to heat shock protein genes could impact protein processing and consequently diminish the vitality of aging lotus seeds. Moreover, an expansion in the number of seed maturation and defense response genes was observed in the lotus genome compared with 11 other species, which might represent an adaptive strategy against long-term adverse storage conditions. Overall, these findings are crucial for understanding the mechanisms underlying lotus seed longevity and may inform future improvements in the extended storage periods of seed crops.This study uncovers the mechanisms behind lotus seed longevity, emphasizing the robust pericarp structure, nutrient reserves in the cotyledons, and unique gene expansions that support stress adaptation and prolonged storage viability.