This paper investigates the impacts of epoxy material viscosity and different gold wire configurations on the total maximum deformation, maximum von Mises stress, and maximum equivalent elastic strain on the light-emitting diode (LED) encapsulation process. The simulation of the LED encapsulation process employed the Volume of Fluid (VOF), Fluid–Structure Interaction (FSI), and System Coupling methods within ANSYS software. The simulation results for an epoxy molding compound (EMC) with viscosity of 0.448 kg/m·s were validated by an experiment. A grid independence test was run to determine the minimum mesh refinement required for the simulation. The results revealed that the final fluid profile of the EMC at 0.448 kg/m·s conformed more closely to the experimental results than the other epoxies. The overall best performance of the wire configuration to the EMC on the LED encapsulation process, in descending order, was the square-loop, triangle-loop, S-loop, Q-loop, and M-loop. This study contributes to understanding the effects of epoxy materials and various gold wire configurations on key mechanical parameters in the LED encapsulation process, hence guiding LED manufacturers in selecting optimal epoxy materials and wire configurations to improve process reliability and performance.