The surface effect in binary nanoparticles (NPs) is known as one of the origins from which extraordinary properties are derived. However, how the surface conditions of a binary NP affect its structure, phase, and property remains unclear. In this work, we use PbBi binary NPs as an example to perform an investigation on this issue. Alloy PbBi NPs with ultra-clean surfaces and a solid-solution phase are fabricated using a delicate evaporation-and-deposition (EAD) method inside a transmission electron microscope and later treated in situ in vacuum or ex situ in air to have different surface conditions. Their shape and phase evolution during structure relaxation are then monitored and compared. It is found that the PbBi NPs with different surface conditions undergo discrepant evolution scenarios. The ones with clean surfaces show a featured transition route from a spherical shape with a uniform phase to a faceted Janus shape with a separation phase, while the ones with thin surface oxidation present contrastive phase segregations confined inside the NPs, forming core−shell structures. Upon further oxidation, dealloying occurs in the alloy phase at the expense of depleting Pb atoms, resulting in featured heterogeneous interfaces and core−shell Bi@PbO x NPs, respectively. The findings here provide direct evidence for understanding the role of surfaces in determining the structure and phase evolutions in nanoalloys, thereby providing knowledge for revealing the stability of binary NPs in applications such as catalysis.