A pulse tube refrigerator (PTR) was developed to operate at different cooling capacities to meet the requirements of various applications. Changes in the thermal loads or the long operating time of the PTR will influence the cold conditions (cold‐end temperature and heat load), leading to a deviation of the cooling performance from the optimal design conditions. The basic principles of the mass flow characteristics of the PTR are constructed based on enthalpy phase modulation, which is helpful for comprehending the relationships between cold‐end parameters and other parameters. A REGEN model is introduced in which different mass flows at the cold‐end are considered to simulate the effects of the cold‐end parameters on the performance of the regenerator. The influences of the cold‐end temperature and heat load on the cooling performance are investigated by using a coupling model of a DeltaEC model and a REGEN model. In addition, some experiments are performed on a PTR working at different cold‐end temperatures and heat load. The experimental results are in good agreement with the simulation results. The cooling performance of the PTR is influenced by the average pressure and operating frequency of different cooling states. Relative Carnot efficiencies of 12.2% for 4 W@60 K with a specific power of 33 W/W and 16.1% for 15 W @120 K with a specific power of 9 W/W can be achieved by the PTR using different operating parameters.