New developments in high temperature ceramic materials technology have focused on obtaining nanocomposite materials with nanoscale features for an optimal control of thermal and mechanical properties. One example is the silicon carbide (SiC)–silicon nitride nanocomposites with nanosized SiC particles placed either in microsized grains or along grain boundaries (GBs). This work focuses on analyzing the influence of GBs, interfaces, and impurities on thermal and mechanical properties of a set of nanocomposites at three different temperatures (300 K, 900 K, and 1500 K). Nanocomposite thermal conductivity values predicted in this study are smaller in comparison to the bulk values . Even with the volume fraction of SiC phase being limited to maximum 40%, it is shown that the thermal conductivity values could be reduced to less than those of the bulk SiC phase by microstructural feature arrangement. Nanocomposite phonon spectral density values show a short rage structural order indicating a high degree of diffused phonon reflection. Visual analyses of the atomistic arrangements did not reveal any loss of crystallinity in the nanocomposites at high temperatures. This indicates that structural arrangement, not the phase change, is a factor controlling thermal conduction as a function of temperature. The nanocomposite deformation mechanism is a trade-off between the stress concentration caused by SiC particles and GB sliding. The temperature increase tends to work in favor of GB sliding leading to softening of structures. However, microstructural strength increases with increase in temperature when GBs are absent. GBs also contribute to reduction in thermal conductivity as well as increase in fracture strength. Replacement of sharp GBs by diffused GBs having C/N impurities, lowered thermal conductivity, and increased fracture strength. Decrease in interfaces by removal of SiC particles tends to favor an increase in thermal conductivity as well as fracture resistance. Overall, it is shown that for high temperature mechanical strength improvement, judicious placement of SiC particles and optimal control of GB atomic volume fraction are the main controlling factors.