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Molecular dynamics (MD) method is an important simulation tool, but its results are always doubtful due to its unrealistic high strain rates.In this paper, a hybrid quasi-static atomistic simulation method at finite temperature is developed, which combines the advantages of MD for thermal equilibrium and atomic-scale finite element method (AFEM) for efficient equilibration.Some temperature effects are embedded in static AFEM simulation by applying the virtual and equivalent thermal disturbance forces extracted from MD.Alternatively performing MD and AFEM can quickly obtain a series of thermodynamic equilibrium configurations such that a quasi-static process is modeled.Moreover, a stirring-accelerated MD/AFEM fast relaxation approach is proposed, in which the atomic forces and velocities are randomly exchanged to artificially accelerate the "slow processes" such as mechanical wave propagation and thermal diffusion.The extraordinary efficiency of the proposed methods is demonstrated by numerical examples on single wall carbon nanotubes.