Light-emitting organic semiconductors have attracted considerable attention for the nanoscale fabrication of organic-based displays and their potential application in optoelectronics, plasmonics, and photonics. In this study, core-shell hybrid nanostructures of organic rubrene coated on Ag nanoparticles (NPs) have been synthesized using a chemical reduction method. The thickness of the rubrene shell was 2.6–6.0 nm and the diameter of the Ag core was 30–70 nm. The optical and structural properties of the Ag/rubrene core-shell NPs were tuned by hydrothermal (HT) treatment at 190 °C. The Ag/rubrene core-shell NPs were characterized by high-resolution transmission electron microscopy and energy-dispersive X-ray (EDX) spectroscopy before and after the HT treatment, and their structural properties were confirmed through X-ray diffraction (XRD) analysis. XRD peaks related to an orthorhombic phase were observed along with the original triclinic crystal structure of the rubrene shell, and the triclinic crystal domain size increased from 28.2 nm to 30.8 nm owing to the HT treatment. Interestingly, the green light emission (λem = 550 nm) of the Ag/rubrene core-shell NPs changed to blue light emission (λem = 425 nm), increasing in intensity through the HT treatment. This is caused by the crystal change with H-type aggregation and enhanced energy transfer from a surface plasmon resonance.