Pathological protein aggregation and synaptic dysfunction are major contributors to neurodegenerative disorders. However, understanding disease-relevant protein aggregation, such as Beta-amyloid, Alpha-synuclein and Tau aggregation within synapses, remains limited. To address this, we present a novel method for visualizing protein aggregates in individual synaptosomes. We combined Single-molecule Pull Down (SiMPull) and direct Stochastic Optical Reconstruction Microscopy (dSTORM), to immobilize individual synaptosomes and characterize single aggregates within them with ~20nm spatial resolution. We validated the method with mouse models of neurodegenerative diseases and post-mortem human brain tissues. Our method offers a valuable tool for decoding molecular triggers underlying neurodegeneration at an early stage and provides new insights into developing earlier therapeutic strategies.