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Learning and memory are fundamental cognitive functions that rely on precise molecular and cellular mechanisms. At the synaptic level, the nanoscale organization of synaptic proteins plays a crucial role in regulating synaptic transmission and plasticity. Super-resolution microscopy techniques, including dSTORM and DNA-PAINT, have advanced our understanding of how glutamate receptors, specifically AMPA and NMDA receptors, form distinct nanodomains that dynamically reorganize in response to neuronal activity. Our research proposes a novel mechanism in which liquid-liquid phase-separated protein complexes contribute to the formation and stability of these structures, highlighting the molecular mechanisms of synaptic nanodomain formation and the dynamic modulation of receptor clustering and spatial organization. Ultimately, these insights will inform broader applications in life sciences, enhancing our understanding of cellular organization and signaling.