Circadian rhythm disorder (CRD) in space flight can lead to memory impairment, performance decrements and adverse health outcomes, the main manifestations of which are circadian desynchronization, sleep loss and insomnia. Sleep deprivation (SD) provide the means to evaluate these effects and the risks associated with CRD on ground. Gastrodia elata Blume (GEB) has beneficial effects on the treatment of sleep disturbances and memory loss. Fresh GEB (FG), an unprocessed raw tuber of GEB, has been used as functional health food in Asian countries for a long time. However, the research report of FG to ameliorate memory impairment caused by insomnia or lack of sleep is meager. In this study, ICR male mice were sleep-deprived continuously and water extract of FG (WFG) was orally administrated (3 and 9 g/kg/d, i.g) during the SD process lasted for 25 days, except control and model groups gavage administration with water, positive control group with modafinil (MOD, 0.1 g/kg/d, i.g). We studied the effect of WFG on CRD-induced learning and memory impairment using a set of behavioral analyses including the object location recognition test (OLRT), novel object recognition test (NORT), and the passive avoidance test (PAT). In addition, oxidative stress parameters were assessed by measuring the malondialdehyde (MDA) and superoxide dismutase (SOD) reactivity in serum and hippocampus. Our results revealed that SD decreased discrimination index (DI) in OLRT and NORT, with shorter latency into the dark chamber in PAT. Both WFG and MOD treatment can reverse these changes (P < 0.05). We concluded that WFG treatment improve CRD-induced learning and memory impairment and oxidative stress damage which makes FG a promising candidate as herbal health product of memory decline in CRD.