Nanofluid (NF) as a new type of high thermal conductivity fluid, macroscopic research methods can only observe the macroscopic change of thermal conductivity of NF, but cannot further reveal the microscopic mechanism of nanoparticles. In this paper, the microscopic mechanism of thermal conductivity enhancement of NF was simulated based on non-equilibrium molecular dynamics method (NEMD), and the thermal conductivities of argon-based gold (Au–Ar) NF with different volume fractions and Au nanoparticle sizes are simulated separately, and the radial distribution functions, system densities, and tracking atom trajectories are computed to explore the mechanism of the action of the change in thermal conductivity of the nanofluids induced by nanoparticles at the microscopic level. It was found that the thermal conductivity of Au–Ar–NF system is positively correlated with the volume fraction of nanoparticles and negatively correlated with the particle size. When the NP particle size was 0.8 nm and the volume fraction was 6.0%, the NF thermal conductivity increased by 65.7% compared to the base solution. The key finding of the study was that the underlying liquid atoms on the surface of the nanoparticles form a non-fugitive adsorption layer, and that their arrangement resembles the ordered arrangement of a solid. In the model with r (NP) = 0.8 nm, the highest thermal conductivity was 1.21 times that of the base solution, and the thickness of the adsorption layer on the particle surface was about 0.35 nm. Generally speaking, the addition of nanoparticles alters the atomic configuration of NF, resulting in NF displaying a solid-like microstructure, which significantly increases the thermal conductivity of NF.