For three-dimensional multi-layer molecularly thin-film lubrication system with elastic substrates, roles of hysteresis on tribological properties are investigated by using the multiscale simulation method. It is found that multiple stick-slip transitions with/without hysteresis loops appear in a sliding process and form a quasi-periodic progress with lattice distance. For the few-/multi-layer thin-film lubrication system, as the load increases, the hysteresis length monotonously increases/tends to keep constant. The hysteresis is mainly caused by the relaxation of metastable states of solid atoms in the elastic substrates, which delays the system back to its equilibrium states. In the quasi-periodic shearing progress, the effective elastic coefficients and the hysteresis lengths approximately remain unchanged, which reveals that although the hysteresis loops with the same lengths appear in the sliding process, the total systematic energy is still conserved. These findings not only provide a profound understanding of roles of hysteresis in the thin-film lubrication system but also show the effects of film layers and loads on the systematic tribological properties, which are of great significance for practical applications.