Microglia are the primary immune cells in the central nervous system. Microglia typically exist in a "resting" state in the healthy brain, with ramified processes dynamically exploring the surrounding microenvironment. They become "activated" under pathological conditions with marked changes in morphology. However, it remains poorly understood about the regulation of their morphology dynamics. Here, using in vivo time-lapse imaging and 3-dimensional morphology analysis of microglia in intact zebrafish larvae, we find that β-arrestin1, a multifunctional protein involved in various signal transductions, cell-autonomously regulates the microglia morphology. Knockdown of β-arrestin1 increased the volume size and process number of microglia while reduced deformation speed under resting state. Meanwhile, β-arrestin1 down-regulation led to a high frequency of phagocytic probability of microglia. These defects were partially rescued by over-expressing human β-arrestin1 in microglia. Together, our study indicates that microglial dynamics at resting state can be regulated cell-autonomously by β-arrestin1 signalling.