We present an investigation of the capillary instability of nanometer-sized surface-tension-driven flow using molecular dynamics (MD) simulations with Lennard-Jones fluid. Unstable motions of a liquid nanojet are successfully simulated and it is found that the thermal fluctuation, which is significant in a nanoscale system, is the most important factor for various breakup scenarios of a nanojet. The nanojet diameter at the nozzle outlet is varied to show the effect of size on the rupture phenomena and the formation of small droplets. Numerical results for the rupture time and the growth rate of spherical droplets are compared with those of various classical linear instability theories. Even though the MD simulation results for the growth rate of the droplets are close to those predicted by the classical instability theories, the former are shown to be independent of the wave number unlike the latter. Therefore, the classical continuum-based theories may not be applicable to studying the instability of nanoscale systems.