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This paper reports novel findings of an investigation of pH-tuned morphological changes in a core-shell gold nanoparticle assembly derived from hydrogen-bonding at the encapsulating shells. Our strategy couples the selective assembly of such hydrogen-bonding-linked nanoparticles at patterned substrates with the capability of atomic force microscopy to detect the nanostructural changes in the pH-tuned interfacial process. The selective assembly on a monolayer-patterned substrate provided an ideal imaging platform with an internal standard from the unassembled areas. The detection of significant and reversible changes of both friction and height in the nanoparticle-assembled areas provided new insights into understanding of ionic fluxes and solvation effect within the nanoporous structure, which have important implications to the design of nanoparticle-based interfaces for nanostructured catalysis and molecular recognition.