Abstract: In order to investigate the effects of cysteine (Cys) treatment in preserving quality and antioxidant activities of Flammulina velutipes during low temperature storage, fresh Flammulina velutipes were pretreated with 15 mmol/L cysteine and clear water at 25 ℃ for 20 min before storage for 12 d at 2~3 ℃, and The physical and chemical indexes were tested regularly. The results showed that 15 mmol/L cysteine treatment could restrain the respiration intensity and delay browning degree of fresh mushroom. At the same time, cysteine treatment could reduce the rate of decline of soluble solids and soluble protein. And the relative conductivity could be kept at low state in cysteine treated mushroom. And cysteine treatment significantly controlled the activity of the polyphenol oxidase (PPO) and could down-regulate the activity of peroxidase (POD). In addition, cysteine treatment had reserved thephenolic compound and ascorbic acid content. At 12 days of shelf-life, the activities of PPO and POD in cysteine treatment group decreased 13.78% and 26.49% compared with the control group, respectively, and the contents of total phenol and ascorbic acid by cysteine treated were 1.12 and 1.37 times of those in control group. Moreover, it could maintain higher levels of superoxide dismutase (SOD) and glutathione reductase (GR) activity along with superior 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging capacity. However, it had no significant difference on the weight loss rate between the two treatment groups. The correlation analysis showed that the correlation coefficients between respiratory intensity and SOD activity and DPPH scavenging rate in the treatment group were −0.951 and −0.903, respectively, and showed a significant negative correlation. In conclusion, cysteine treatment could reduce the metabolic rate of internal substances of Flammulina velutipes, maintain higher antioxidant capacity and sensory quality during preserved period.