Instability and rupture dynamics of a liquid nano-thread, subjected to external hydrodynamic perturbations, are captured by a stochastic lubrication equation (SLE) incorporating thermal fluctuations via Gaussian white noise. Linear instability analysis of the SLE is conducted to derive the spectra and distribution functions of thermal capillary waves influenced by external perturbations and thermal fluctuations. The SLE is also solved numerically using a second-order finite difference method with a correlated noise model. Both theoretical and numerical solutions, validated through molecular dynamics, indicate that surface tension forces due to specific external perturbations overcome the random effects of thermal fluctuations, determining both the thermal capillary waves and the evolution of perturbation growth. The results also show two distinct regimes: (i) the hydrodynamic regime, where external perturbations dominate, leading to uniform ruptures, and (ii) the thermal-fluctuation regime, where external perturbations are surpassed by thermal fluctuations, resulting in non-uniform ruptures. The transition between these regimes, modelled by a criterion developed from linear instability theory, exhibits a strong dependence on the amplitudes and wavenumbers of the external perturbations.