Microglial activation is the initial pathological event that occurs in demyelination, a prevalent feature in various neurological diseases. G protein-coupled estrogen receptor (GPER1), which is highly expressed in microglia, has been reported to reduce myelin damage. However, the precise molecular mechanisms involved remain unclear. In this study, the cuprizone (CPZ) -induced demyelination model was used to investigate the relationship between GPER1 and myelin sheath injury and its mechanism. The results demonstrated that GPER1 deficiency exacerbated cognitive impairment in mice. Along with more severe myelin damage as well as fewer oligodendrocytes. Moreover, GPER1 deficiency not only directly reduced the number of microglia in CPZ mice, but also caused iron ions overload in microglia of myelin debris induced in vitro. Transcriptomic, molecular biological, and morphological analyses revealed that microglial ferroptosis caused by GPER1 deficiency contributes to the reduction of microglia number. In summary, these findings revealed that GPER1 can regulate demyelination through ferroptosis of microglia.