The thermodynamic behavior of gas parcels in the key parts of the pulse tube cryocooler (PTC) is studied. The refrigeration mechanism of PTCs under different cold end phase angles is revealed by analyzing and comparing the heat transfer characteristics of the gas parcels at both sides of the cold end heat exchanger. Results show that the cold end phase angle, an important parameter of the PTC, determines the cooling performance of the PTC by affecting the heat transfer characteristics of the gas parcels in a cycle. In PTCs with a cold end phase angle normally between -30 degrees and 60 degrees, the gases pump heat from the cold end heat exchanger to the aftercooler all the way through the regenerator. In contrast, for the basic PTC with a cold end phase angle close to 90 degrees, the heat transfer direction is reversed, the gases pump heat from the cold end heat exchanger to the hot end heat exchanger all the way through the pulse tube. This study unifies the various perspectives on the PTC's refrigeration mechanism by revealing the inherent effect of the cold end phase angle, indicating that enhancing the heat pumping function of the gas in the regenerator is an essential way to improve the cooling performance. (C) 2016 Elsevier Ltd. All rights reserved.