This paper investigates the vaporization process of two nano-scale liquid threads coexisting in a periodic fundamental cell by molecular dynamics (MD) simulation. The influences of liquid thread radius, fundamental cell length, and relative position of the two threads are discussed. Snapshots of molecules, the number of liquid particles formed, and density field are analyzed. Two linear stability criteria, namely, Rayleigh’s stability criterion and Kim’s stability criterion, are accessed for their validity in molecular scale. It is found that more liquid particles are formed when the separation of the two threads is larger. Moreover, vaporization is slower when the two liquid threads are close to each other. It is also found that the trends of Rayleigh’s stability criterion and Kim’s stability criterion agree with MD simulation results. However, when the two threads coalesce into a single thread and remain intact, the critical wavelength of perturbation may be increased and the stable domain is broadened. Under such a situation, Rayleigh’s stability criterion and Kim’s stability criterion underpredict the stable domain.