To obtain an accurate thermal conductivity of Ag2Se considering heat‐flux effects, computational requirements such as simulation times and number of atoms are investigated for two methods: the Green–Kubo (GK) formula in equilibrium molecular dynamics (EMD) simulations and perturbed MD (pMD). An empirical interatomic potential is used, which reproduces both the superionic and nonsuperionic phases of Ag2Se. It is found that the accurate thermal conductivity based on the GK formula requires at least the correlation time of 12 ps, the simulation time of 24 ns, and the number of atoms of 3000. In contrast, for the pMD, the simulation time of ≈1.2 ns is needed to obtain a comparable thermal conductivity. It is also confirmed that the heat flux must be considered in MD simulations to qualitatively reproduce the temperature dependence of thermal conductivity observed experimentally.