This paper studied the active oxygen scavenging system of Cupressus funebris seedlings under drought condition and the recovery capability of the system after re-watering, aimed to understand the adaptation mechanisms of C. funebris to the 'drought and re-watering' environment in Karst area. With the increasing time of drought stress, the seedling's relative water content (RWC) decreased, soluble protein concentration increased first and decreased then, and malondialdehyde (MDA) content increased consistently. The MDA content recovered to the level of the control (CK) when re-watering was implemented within 2 weeks of drought, but could not when the re-watering was made after 4 and 6 weeks of drought. Under drought stress, the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) increased consistently. After rewatering, the SOD activity had somewhat decrease but still remained at a higher level than the CK, and the POD and CAT activities decreased to the CK level when suffered mild stress but had less decrement when suffered severe stress. It was concluded that C. funebris seedlings could resist mild drought stress via increasing their soluble protein concentration and inhibiting membrane lipid peroxidation, but could not resist severe drought stress because of the irreversible damage of their membrane structure.