The increased production and release of organic pollutants due to industrial development has necessitated effective water treatment technologies. In this study, an unprecedented yolk–shell-structured catalyst was developed and evaluated for the oxidative degradation of organic pollutants. Gold nanospheres (AuNSs) encapsulated in mesoporous silica nanocapsules (AuNS@ySiO2) were synthesized via seeded growth and a subsequent selective etching process, and their characteristic properties were analyzed thoroughly. To investigate the catalytic performance of the AuNS@ySiO2/peroxydisulfate (PDS) system, comparative experiments were performed with various control groups of different structures (bulk AuNS suspension, hollow silica nanocapsules without AuNSs, and AuNS-decorated silica nanoparticles) with phenol as the target compound. The AuNS@ySiO2/PDS system exhibited outstanding performance in phenol degradation compared to the control groups with an identical amount of AuNSs, which resulted from the enhanced colloidal stability of the AuNSs. A series of experiments to elucidate the mechanism of phenol degradation suggested that electron transfer from phenol to PDS mediated by AuNSs is a highly plausible pathway. Furthermore, in the presence of humic acid, phenol degradation by the AuNS@ySiO2/PDS system was significantly less inhibited compared to the results for the control group (AuNS-decorated silica nanoparticles), owing to the molecular sieving effect of the mesoporous silica shell constituting AuNS@ySiO2. The newly developed yolk–shell-structured catalyst can prospectively be effectively applied in the catalytic oxidation of organic pollutants owing to its unique structural properties and high catalytic activity.