In the past decade, rapid advancements in microtechnology and nanotechnology have propelled modern science and technology into the nanoscale domain, where miniaturization and high integration have found extensive applications across various fields, including industry, biotechnology, and information technology. Mechanisms of nanofluid flow and heat transfer properties have received increasing attention. In the flow and convective heat transfer of fluids at the nanoscale, the shape and dimensions of the surfaces play a crucial role. So, the main purpose of our paper is to investigate the influence of surface roughness with different shapes and quantities on fluid flow and convective heat transfer. In this study, we have chosen argon atoms as the fluid and used copper atoms to simulate the nanochannel walls. In order to investigate the influence of the shape and quantity of roughness on the convective heat transfer of fluids within nanochannels, we computed and analyzed the velocity, temperature, and density distributions of fluids inside channels with triangular, hemispherical, and rectangular roughness. Through simulation results, we found that triangular, hemispherical, and rectangular surface roughness at the same height can result in differences in temperature and velocity of the fluid within nanochannels. With a nanochannel roughness number of 5, the temperature and velocity of the fluid at the middle position of the nano-channel for the triangular roughness increased by 6% and 25% compared to the rectangular roughness, and by 4% and 10% compared to the hemispherical roughness. The fluid temperature and velocity are highest in channels with triangular surface roughness and lowest in those with rectangular roughness. Furthermore, increasing the quantity of surface roughness decreases the temperature and velocity of the fluid within nanochannels. When the quantity of rectangular surface roughness is 5, the fluid temperature within the nanochannel decreases by 12%, and the velocity decreases by 38% compared to a roughness quantity of 1. We also found, through velocity contours, that the presence of roughness increases the local fluid velocity in the rough regions of nanochannels. Roughness also reduces the density fluctuations of the fluid near the walls within the nanochannel. Roughness significantly affects the heat transfer performance of the fluid during its flow, and this influence should not be overlooked. In this study, molecular dynamics theory was employed, and simulations were conducted using the open-source software LAMMPS to investigate the influence of different shapes and quantities of surface roughness on fluid flow within nanochannels. The model in this paper was constructed using the LAMMPS software, and the surface roughness shapes on the walls were implemented as rectangular, hemispherical, and triangular. The wall surfaces were composed of copper atoms, while the fluid consisted of argon atoms. The copper atoms were arranged in a face-centered cubic (FCC) lattice with a lattice constant of 3.615 Å. Similarly, the argon atoms were arranged in a face-centered cubic (FCC) lattice with a lattice constant of 5.62 Å. The interactions between copper atoms were modeled using the EAM (Embedded Atom Method) potential, while the interactions between argon atoms were described using the LJ (Lennard-Jones) potential. The LJ potential was also employed to represent interactions between argon and copper atoms.