•Three types of hybrid nanofluids, composite, Janus and dual nanofluid, have been studied by MD.•The highest TC of composite nanofluids in mono-particle system is attributed to Brownian motion.•Why a moderate DOL has a larger TC is discussed.•Enhanced reliability of TC results is achieved from the multi-particle systems including >32 nanoparticles. More and more applications of hybrid nanofluids are emerging in various fields such as energy engineering, chemical engineering, and automotive engineering. However, the existing literature only employs the term "synergistic effect" to explain the improvement of thermal conductivity of hybrid nanofluids. In order to elucidate the underlying reasons behind the improvement in thermal conductivity of hybrid nanofluids compared to that of conventional ones (mono nanofluids), molecular dynamics simulations were conducted to examine three types of hybrid nanofluids, including Ag-Cu nanocomposites, Au-Cu Janus nanoparticles, and Ag-Cu binary nanoparticles. The results suggest that hybrid nanofluids including Ag-Cu nanocomposites, Au-Cu Janus nanoparticles, and Ag-Cu binary nanoparticles improve the thermal conductivity of 2 vol% nanofluid by 34.3 %, 12.1 %, and 10.4 %, respectively, compared to Cu monofluid. The improvement in thermal conductivity for hybrid nanofluids containing nanocomposites in single-particle systems can be attributed primarily to the stronger Brownian motion, while the improvement in thermal conductivity for hybrid nanofluids containing Au-Cu Janus nanoparticles and Ag-Cu binary nanoparticles is due to the looser aggregation morphology in multi-particle systems. This observation allows us to appreciate the significance of aggregation morphology as a crucial mechanism when considering interactions between nanoparticles. It provides a theoretical basis for the preparation of high-performance nanofluids as heat transfer media.