The use of microscale heat generating or heat transfer equipment with higher capacity and smaller dimensions requires more accurate management and better disposal of their produced heat. This makes the necessity of designing and manufacturing superconductors completely clear. In the meantime, the nano-grooved flat plate heat pipes (FPHP) have gained the industry’s attention. Due to the provision of the conditions for manufacturing devices on a micro scale, it is possible to integrate this type of heat pipe with other microscale devices. In the meantime, understanding their behavior on small scales requires more studies. In this paper, the effect of using barriers to improve the thermal performance of a nano FPHP (1050×220×95Å) is evaluated. Simulations are performed on a molecular scale through molecular dynamics (MD) simulations using LAMMPS® software. Platinum (Pt), copper (Cu), and aluminum (Al) are used for HP’s body. In addition, argon (Ar), water (H2O), and ethanol (EtOH) are used as working fluids. The results show that increasing the number of barriers leads to improved thermal performance. Different cases include different teeth called barriers augmented inside HP are simulated. The combination of Cu-EtOH showed the best thermal performance (about 18% better than other cases). Cubical barriers have more heat flux improvement than conical ones (from 3.5% up to about 10.7%). Among the three fluids used, EtOH leads to a better heat flux (about 6% for Pt and up to 15% for Cu). Using 24 barriers, a very favorable result of 1992 W/cm2 heat flux is achieved. In this case, the minimum heat flux is obtained by using Pt and Ar and is 1609 W/cm2. Using Ar and the cub shape barriers, the highest mass transfer rates for Pt, Cu, and Al are about 35.2%, 38.9%, and 38%, respectively.