We have explored the effectiveness of Geant4 by using it to simulate phonon conduction in Sn Host with Si Nanowire Interface. Our Monte Carlo Simulation shows that the effectiveness of the phonon conduction Geant4 simulation increases when the system attained a steady state of 100 time steps. We have simulated phonon conduction in Sn host with Si nanowire interface using a Geant4Condensed Matter Physics Monte Carlo simulation toolkit in a low cost and less powerful processing computer machine. In the simulation, phonons were displaced inside a computation domain from their initial positions with the velocities and direction vectors assigned to them. A time step was selected so that a phonon can move at most the length of one sub-cell in one time step. Our phonon conduction analysis of SiSn based alloy using Geant4 showed performance enhancement and reasonable predicted thermal values. Numerical predictions of the thermal profile simulations of the values of the temperature in each cell were all within ten percent of the average temperature of Silicon – Tin.