Surface heterogeneity of a metal nanoparticle is typically regarded as boundary defects and various crystalline facets. While organic capping ligands of a single type are assumed to be homogeneously distributed on the nanoparticle surface, heterogeneous surface coverage of citrate molecules on individual facets of gold nanoparticles (AuNPs) is revealed. Pt metallic clusters with 2 nm in diameter, epitaxially grown on the surface of AuNPs by chemical reaction and imaged by high‐resolution transmission electron microscopy, are utilized as negative‐imaging probes for densely packed adlayers where the underneath gold surface may not be accessible for Pt deposition. At pH > 5.0, citrate anions form only a loosely packed layer. At pH 4.5, citrates and citric acids form both loosely packed and densely packed layers that appear phase separated, and the densely packed domain as small as 5 nm × 5 nm is likely composed of fully protonated citric acids. IR spectra indicate that citric acid binds to a surface Au adatom through the oxygen atom of the central hydroxyl group, and similarly, citrate anions bind to Au adatoms through the carboxylate oxygen atom. This study also reveals the role of Au adatom in the adsorption of citrate species on the metallic surface of AuNPs.