The complex organizations of amino acid residues on protein surfaces give rise to a wide space of functions for proteins. Great efforts are devoted in biology to understand such structure-property relationships. Many advanced characterization techniques have been developed for this purpose. Nanomaterials are regarded as a close resemblance to proteins, as they share similar sizes and, when coated with different types of ligand molecules, can present patchy surfaces (e.g. stripe-like, patchy, or Janus) that bear some similarities to the surfaces of proteins. So far, most characterization methods developed for nanoparticles come from classic material sciences and consequently deliver a precise description of the inorganic and well defined core of the nanoparticles. Yet big challenges remain to accurately describe the morphologies of the ligand shell of nanoparticles that is closer to a biological entity rather than small sized materials. This thesis establishes two new techniques for the characterization of the morphology of the ligand shell of nanoparticles. The first stems directly from structural biology, i.e. small angle neutron scattering combined with ab initio reconstructions. 3D models could be obtained by fitting the scattering data, allowing for the quantitative determination of different morphologies. The second one is based on the statistical analysis of the MALDI-TOF MS spectra. Adopting Monte Carlo calculations, the structures of mixed ligands could be visualized by fitting the fragmentation patterns that represents a sampling of the nanoparticle surfaces. Thanks to the advancement in characterization provided by these newly development methods, two phenomena are studied in this thesis. First, the evolution of the ligand shell morphology during a ligand replacement reaction called place-exchange is uncovered for the first time. Also the evolution of the ligand shell morphology upon gentle heating is uncovered. These results provide a new way to control the morphology of the nanoparticle ligand shells. Second, an in-depth study of the water structure around patchy surfaces is presented. Two nanoparticles with the same core size and composition but varying in the ligand shell structures are synthesized. The morphologies of the heterogeneous nanoparticle surfaces on top of chemical nature are thus directly correlated to the structure of interfacial water. This work offers molecular explanation on the structural factor in the interfacial energy of multiple component systems, which has not been discussed in physical chemistry textbooks before. This latter work offers new insights on how patchy nanoparticles could be used as model systems to understand the interfacial properties of proteins, which are often very difficult to be studied directly due to the complex and dynamic structures of the proteins.