Molecular dynamics simulation is used to investigate the flow characteristics of Cu–Ar nanofluids considering the influence of nanoparticle size and nanoparticle aggregation. Nanofluids viscosity is calculated by equilibrium molecular dynamics based on Green–Kubo equation. Results demonstrate that the viscosity of nanofluids decreases with the increase of nanoparticle size. In addition, nanoparticle aggregation results in the increase of the nanofluids viscosity. Compared with nanoparticle size, nanoparticle aggregation has a larger impact on viscosity. Nanofluids flowing in parallel-plate nanochannels are simulated. The velocity profiles are studied through three nanoparticle sizes (11.55, 14.55, and 18.33 Å) and four nanoparticle aggregate configurations. Results show that the velocity profile of 14.55 Å nanoparticle size is larger than that of other two nanoparticle sizes. As for four nanoparticles, the nanoparticles clustering as a line leads to the maximum velocity profile, while the nanoparticles clustering as a cube causes the minimum velocity profile. Compared with viscosity, nanoparticle aggregation has a greater effect on the velocity profile. When the nanoparticles are evenly distributed, the influence of viscosity on velocity profiles is dominant. Otherwise, the aggregation, aggregate configuration, and distribution of nanoparticles have a dominant impact on the flow characteristics of nanofluids.