Molecular dynamics (MD) simulations have been performed to provide the basic knowledge of nanofluidics and its applications at the molecular level. A nonequilibrium molecular dynamics (NEMD) code was developed and verified by comparing a micro Poiseuille flow with the classical Navier–Stokes solution with nonslip wall boundary conditions. Liquid argon fluids in a platinum nanotube were simulated to characterize the homogeneous fluid system. Also, positively charged particles were mixed with solvent particles to study the non-Newtonian behavior of the heterogeneous fluid. At equilibration state, the macroscopic parameters were calculated using the statistical calculation. As an application of MD simulation, the nanojetting mechanism was identified by simulating the full process of droplet ejection, breakup, wetting on the surface, and natural drying. For an electrowetting phenomenon, a fluid droplet with positive charges moving on the ultrathin film with negative charges was simulated and then compared to the macroscopic experiments. A conceptual nanopumping system using the electrowetting phenomenon was also simulated to prove its feasibility. The molecular dynamics code developed here showed its potential applicability to the novel concept design of nano- and microelectromechanical systems.