In this study we use molecular dynamics (MD) simulations to describe the nanopumping process of Boron Nitride Nanotube (BNNT) with fullerene molecule displacement for the first time. Technically, for the simulation of BNNT and fullerene structures, we used Tersoff force-field. The result of the equilibrium process of these structures shows the excellent stability of them which this atomic behavior arises from the appropriate settings in our MD simulations. Further, to describe the BNNT nanopumping process, we calculate the velocity and translational/rotational kinetic energy of fullerene molecule. Numerically, by increasing of simulated structures temperature from 275 K to 350 K, the nanopumping time varies from 9.31 ps to 8.55 ps, respectively. Further, the atomic wave producing in BNNT is an important parameter for nanopumping process and we decrease the nanopumpint time to 7.79 ps by this atomic parameter optimization.