Rational assembly of nanoparticles is of vital importance for exploring fundamental electronic and optical properties and for constructing novel nanoscale devices. Through controlling aggregation kinetics, dimers and trimers of gold nanoparticles were generated and encapsulated with polymer by using a one-pot synthesis that involved simple heating and cooling. Dimers of gold nanoparticles were enriched from the resulting solution by centrifugation. The polymer shells maintain the stability of the nanoparticle organization, preventing aggregation and disintegration during subsequent purification, enrichment, and application. A typical enriched sample showed that the dimer population reached 61% among 989 nanoparticles surveyed. In a proof-of-concept application, the gold nanoparticle dimers were used as catalyst to guide the growth of dimeric zinc oxide nanowires. Nanowire dimers with unprecedented narrow spacing (20 to 60 nm) were achieved using a vapor transport growth method; dimeric nanowire population reached approximately 25%.