Simulation of thermal properties of graphene hetero-nanosheets is a key step in understanding their performance in nano-electronics where thermal loads and shocks are highly likely. Herein we combine graphene and boron-carbide nanosheets (BC3N) heterogeneous structures to obtain BC3N-graphene hetero-nanosheet (BC3GrHs) as a model semiconductor with tunable properties. Poor thermal properties of such heterostructures would curb their long-term practice. BC3GrHs may be imperfect with grain boundaries comprising non-hexagonal rings, heptagons, and pentagons as topological defects. Therefore, a realistic picture of the thermal properties of BC3GrHs necessitates consideration of grain boundaries of heptagon-pentagon defect pairs. Herein thermal properties of BC3GrHs with various defects were evaluated applying molecular dynamic (MD) simulation. First, temperature profiles along BC3GrHs interface with symmetric and asymmetric pentagon-heptagon pairs at 300 K, ΔT = 40 K, and zero strain were compared. Next, the effect of temperature, strain, and temperature gradient (ΔT) on Kaptiza resistance (interfacial thermal resistance at the grain boundary) was visualized. It was found that Kapitza resistance increases upon an increase of defect density in the grain boundary. Besides, among symmetric grain boundaries, 5–7–6–6 and 5–7–5–7 defect pairs showed the lowest (2 × 10–10 m2 K W−1) and highest (4.9 × 10–10 m2 K W−1) values of Kapitza resistance, respectively. Regarding parameters affecting Kapitza resistance, increased temperature and strain caused the rise and drop in Kaptiza thermal resistance, respectively. However, lengthier nanosheets had lower Kapitza thermal resistance. Moreover, changes in temperature gradient had a negligible effect on the Kapitza resistance.