This paper investigated the optical and thermal performance of the nitride-based ultraviolet light-emitting diodes fabricated by the eutectic flip-chip method. A new packaging structure was proposed by introducing a thin encapsulation layer doped with 0.4 wt% AlN nanoparticles (NPs) and uniform quartz lens simultaneously. Experimental results showed that the packaging structure proposed in this paper could significantly enhance the light output power, reduce the junction temperature, and increase the emission angle compared with the encapsulation layer consisting silicone only. When the NPs concentration increased from 0.1 to 0.4 wt%, the light output power increased from 7.6% to 17.4% at the forward current of 800 mA. Meanwhile, the junction temperature decreased by 5.7 °C, while the emission angle increased by 11.3°. What is more, it was found that the enhancement of light output power depended on the NPs concentration and showed the maximum at the concentration of 0.4 wt%. The enhanced light output power was attributed to the additional light scattering and the increased average refractive index resulted from the NPs introduced in the proposed package structure.