Glia, which are nonneuronal cells in the central nervous system, include astrocytes, microglia, and oligodendrocyte lineage cells. Historically, their passive roles in maintaining central nervous system function—such as supplying substrates for neuronal energy, buffering neurotransmitters, and improving neural conductance—have been primarily highlighted. Importantly, recent research has revealed that glial cells express genes directly related to controlling synapse nano-organization. In particular, astrocytes have the ability to secrete molecules that induce synapse formation and maturation. They also modulate the structure of synapses by expressing proteins that make direct contact with the synaptic membrane. Moreover, astrocytes can actively eliminate synapses through their phagocytic machinery during development and adulthood, thereby establishing circuit homeostasis. Microglia can also assist in the integration of synapses into the neural circuit and regulate synapse formation, maintenance, and elimination. Here, we review key findings on the mechanisms of glial contributions to synapse nano-organization. We will also discuss how different glial cells contribute to the development and homeostasis of synapses through distinct cellular and molecular pathways in both health and disease.