Spiky and twisted morphologies of organic-inorganic particles found in living systems often perform specific functions that simple spherical particles cannot achieve. These structures result from hierarchical assemblies of molecular and nanoscale units and are characterized by their structural complexity. Due to the nature of stochasticity and coexistence of order and disorder, utilizing these particles as functional materials precise quantification of the property distribution for individual particles. Herein, we present a high-throughput analysis method for single "hedgehog" particles, which exhibit rapid attachment to and isolation of exosomes. We have developed a methodology to effectively isolate each particle and collect multi-dimensional data. Our results demonstrate the size-selective capture of exosomes by the hedgehog particles and provide precise quantification of their interaction kinetics. Our methodology offers a guideline for characterizing functional complex nanoassemblies.