To make the light-emitting diode (LED) more compact and effective, the flip chip solder joint is recommended in LED chip-scale packaging (CSP) with critical functions in mechanical support, heat dissipation, and electrical conductivity. However, the generation of voids always challenges the mechanical strength, thermal stability, and reliability of solder joints. This paper models the 3D random voids generation in the LED flip chip Sn96.5-Ag3.0-Cu0.5 (SAC305) solder joint, and investigates the effect of thermal shock load on its mechanical reliability with both simulations and experiments referring to the JEDEC thermal shock test standard (JESD22-A106B). The results reveal the following: (1) the void rate of the solder joint increases after thermal shock ageing, and its shear strength exponentially degrades. (2) the first principal stress of the solder joint is not obviously increased, however, if the through-hole voids emerged in the corner of solder joints, it will dramatically increase. (3) modelling of the fatigue failure of solder joint with randomly distributed voids utilizes the approximate model to estimate the lifetime, and the experimental results confirm that the absolute prediction error can be controlled around 2.84%.