Light-emitting diode (LED) failure mechanism plays an important role in studying and manufacturing LEDs. In this paper, X-ray perspective instrument is used to carry out the non-invasive and real-time X-ray imaging detection of the representative LED packaging products purchased from 5 Chinese companies. A large number of the welded voids are founded in the thermal pad and the void ratio of thermal pad, which represents the ratio of void area to pad area, is more than 30% for all samples. 1 W warm white light LED of GaN-based vertical via structure is selected to study the mechanism of short-circuit invalidation. The method is carried out by the following steps. Firstly, the surface morphologies of failure samples are compared with those of normal samples by visual observation. Secondly, antistatic electric capacity testing instrument is used to detect the existences of the electrical parameter abnormalities of the failure of non-short-circuit samples. Thirdly, decapsulations are operated on samples by using Silica gel dissolving agent. And the microtopographies of the samples are characterized by optical microscope, energy dispersive spectrometer and scanning electron microscopy. Then the cross-sectional morphologies of failure samples are observed. The failure mechanism can be drawn from the characterizations mentioned above. The study shows that the failure mechanism of the vertical structure of GaN-based vias is that the existences of voids in the Ni-Sn alloy back gold layer and solid-crystal layer reduce the interface bonding strength and thermal conductivity of the LED chip. The heat building-up leads to thermal expansion of the air inside the voids, which increases the electrical stress and thermal stress distribution at the LED chip vias. Long-term heat accumulation and higher electrical stress in the through-hole region, where the chip current density is greatest, lead to the crack and break of GaN epitaxial layer, which is so brittle and fragile, around the through-hole region. It can eventually lead to short-circuit of PN junction and then failure of LED. Back gold layer is the heat-conductive and electric-conductive channel of LED. The concentrations of thermal stress and electrical stress caused by voids in the back gold layer further lead to the uneven current distribution on the chip. This is the main reason why GaN epitaxial layer cracks and breaks. Voids in the back gold layer and solid-crystal layer are the direct and indirect causes of LED short-circuit failure, respectively. Therefore, the packaging process should be standardized to avoid the void occurrence, based on the reasons why voids exist. It can finally improve reliability of LED.