With the rapid development of modern electronic products, efficient thermal management is becoming a global challenge. The interface thermal resistance is the most important factor limiting the high thermal conductivity of thermally conductive nanocomposites. Here, we designed and hydrothermally synthesized a hexagonal boron nitride (BN)/molybdenum disulfide (MoS2) heterostructure with low interfacial thermal resistance, and integrated them into the final BN/MoS2-epoxy nanocomposite. During the hydrothermal reaction, MoS2 grows and wraps on the BN nanosheet, which ensures better interfacial contact. BN nanosheet acts as a structural skeleton and heat transfer channel. MoS2 nanosheets can effectively collect heat due to its large specific surface area. With the infiltration of MoS2, the interfacial thermal resistance between the filler and the polymer matrix can be effectively reduced. The experimental results show that the thermal conductivity of the synthesized BN/MoS2-epoxy nanocomposites was increased from 0.254 W/(m·K) to 0.526 W/(m·K), which is an increasement of 107% as compared to pure epoxy resin. The findings may contribute to the development of new types of high-performance thermal conductivity materials.