Noble metal nanomaterials have emerged as a unique class of materials with wide range of advanced properties. While the metal composition has been thoroughly studied over the past few decades, it was in the later days that researchers have found the surface ligands on the metal core contributes to the functions of nanoparticles. Organic surface ligands influence the properties of inorganic nanostructures across numerous length scales and are responsible for the tailoring of particle morphology during synthesis, modulating optoelectronic properties, and allow for control over interparticle interactions that lead to the assembly of ordered mesoscale materials. Early studies aimed at understanding the role of surface ligands primarily made use of spherical particles and were predicated on the assumption of a homogeneous spatial distribution of ligands across the particle surface. However, even in this prototypical case, it has recently been shown that heterogeneity in the ligand shell. This thesis discusses our platform for observation of heterogenous ligand binding on anisotropic nanoparticles. The in-situ observation of ligands through CryoEM provides solution state depiction of heterogenous ligand binding behavior and allows for quantification of ligand binding probability within few nanometer resolution. I further utilize this platform to draw insights on the mechanism of heterogenous binding behavior, the CryoEM nanoparticle-tag structure provides evidence for the bound-ion pair X-type ligands are binding to nanoparticles surface as an entity rather than through two step process. The static results also provide evidence that the selective binding behavior can be caused by pre-existing ligand shells prevents incoming ligands for steric hindrance as well as by the effect that incoming ligands binds to certain facets stronger enthalpically. I believe this novel platform has great potential for illustrating the ligand binding behavior and will lead to future design of novel nanoparticle structures. Lastly, I showcase an image processing method to localize single atoms in HAADF images. This method has successfully identified the Au single atoms in Au32 cluster HAADF images and proved great opportunity for metal cluster structure characterization and behavior study.