In engineering fields there are such energy transport and or conversion processes in which the resulting quantity is expressed by the dot production of two vectors. For such processes, the reduction of the intersection angle (or phase angle shift) between the two vectors is the most fundamental way for enhancing the processes (field synergy principle). For a pulse tube refrigerator (PTR) its cooling capacity at the hot end is shown to be proportional to the dot production of velocity vector and pressure vector. Detailed numerical analyses are conducted for the PTR to reveal the variation of its cooling capacity with the phase angle shift between the velocity wave and pressure wave. Numerical results clearly reveal the size effect of the orifice and double inlet valve of the PTR on the phase angle shift, and hence, on the PTR cooling capacity. The field synergy principle is further used to determine the optimum length to diameter ratio of the pulse tube and the optimal molar percentage of helium for a PTR using hydrogen/helium mixture as a working medium. Simulation results definitely show that the field synergy principle is a powerful guide to enhance energy conversion and transport processes.