It is of great importance to reveal the refrigeration mechanism at low-temperature around 4 K in pulse tube for improvement of the cooling performance in 4 K pulse tube crycoolers (PTCs). In this paper, the thermo-physical process in 4 K pulse tube was studied analytically from microscopic viewpoint using CFD simulation. The thermodynamic cycles of different gas parcels throughout the pulse tube were investigated. It was found that the real gas characteristics of the helium at the pulse tube cold end manifest more apparently from the central part nearer to the wall outside the boundary layer. Furthermore, it was revealed that boundary layer has the weakened heat loss or helpful effect on refrigeration in phase-shifting 4 K pulse tube operating at low frequency. This research newly provides intensified understanding of the inherent characteristics of 4 K GM-type pulse tube.