Space Lotus No. 36' green lotus seed was chosen as test materials. Their quality and physiological indices were measured after green lotus seed immersed in 75 mg/L and 175 mg/L 6-BA respectively and stored at 4 ℃. The results showed that 175 mg/L 6-BA can alleviate the weight loss rate of green lotus seed during storage and reduce the loss of total soluble solids (TTS) in green lotus seed nut. 175 mg/L 6-BA can delay the brown time of green lotus seed during storage. The brown time of green lotus seed and green lotus seed nut was delayed by 3 days and 6 days, respectively. In addition, 6-BA treatment can delay the increase of malondialdehyde (MDA) content and inhibit the activity of polyphenol oxidase (PPO) and respiration rate in green lotus seed peel. The peak of activities of PAL in green lotus seed peel was delayed by 3 days in 175 mg/L 6-BA treatment group. The 175 mg/L 6-BA treatment can inhibit the aging process of green lotus seed, which is beneficial to maintain fruit quality and improve storage.