We report direct high-resolution monitoring of an evolving mixed nanodomain surface morphology during thiol adsorption on polyvinylpyrrolidone (PVP)-stabilized single crystal gold nanocrystals. The thiol adsorption and replacement dynamics are much more complex than a simple complete substitution of the initial polymer ligand. We observed that during ligand exchange with linear thiol, the nanocrystal surface evolved from an initial 1 nm uniform PVP coating into a remarkably stable network of globular PVP domains 20-100 nm in size and similar to 4 nm in height surrounded by thiol self-assembled monolayers. The final stability of such a mixed thiol PVP surface morphology can possibly be attributed to the interfacial energy reduction from partially solvophilic surfaces and the entropic gain from mixed ligand surface layers. The ligand-exchange dynamics and the unusual equilibrium morphology revealed here provide important insights into both displacement dynamics of surface-bound molecules and the nanoscale peculiarities of surface functionalization of colloidal metal substrates.