The thermal conductivities and glass transition temperatures of polybutadiene crosslinked with randomly distributed sulfur chains having different lengths from mono-sulfur (S1) to octa-sulfur (S8) were investigated. The thermal conductivities of the related models as a function of the heat flux autocorrelation function, applying an equilibrium molecular dynamic (EMD) simulation and the Green–Kubo method, were studied for a wide range of temperatures. The influence of the length of sulfur chains, degree of crosslinking, and molar mass of the crosslinker on the glass transition temperature and final values of thermal conductivities were studied. First, the degree of crosslinking is considered constant for the eight simulation models, from mono-sulfur (S1) to octa-sulfur (S8), while the molar mass of the sulfur is increases. The results show that the thermal conductivities of the crosslinked structure decrease with increasing temperature for each model. Moreover, by increasing the lengths of the sulfur chains and the molar weight of the crosslinker, thermal conductivity increases at a constant temperature. The MD simulation demonstrates that the glass transition temperature and density of the crosslinked structure enhance as the length of the sulfur chains and molar mass of the sulfur increase. Second, the molar weight of sulfur is considered constant in these eight models; therefore, the degree of crosslinking decreases with the increase in the lengths of the sulfur chains. The results show that the thermal conductivities of the crosslinked structure decrease with the increase in the temperature for each model. Moreover, by increasing the lengths of sulfur chains and thus decreasing the degree of crosslinking, the trend in changes in thermal conductivities are almost the same for all of these models, so thermal conductivity is constant for a specific temperature. In addition, the glass transition temperature and density of the crosslinked structure decrease.