In this paper we developed and designed, based on theoretical considerations, a new type of 4 K GM/PT hybrid refrigerators. The upper warm stage of the hybrid refrigerator is a typical GM refrigeration cycle, and the cold stage is a pulse tube refrigerator (PTR), on which is thermodynamically coupled the upper warm stage. Four different types of phase shifting assembly: (1) a cold auxiliary piston that is connected to the displacer of the upper GM refrigerator stage, (2) an orifice with reservoir encircled the cold head of the upper stage, (3) an orifice with double-inlet, and (4) in combination with the cold auxiliary piston, orifice and double-inlet, has been proposed and analyzed for the adjustment of the phase shift between the gas mass flow and pressure in the pulse tube. Numerical simulation is performed to understand the unique thermo-physical features, to reveal the time-dependent dynamic parameters and to quantify the overall cooling performance of the hybrid refrigerator. We rely on a one-dimensional, unsteady compressible flow numerical model that is based on a mixed Eulerian–Lagrangian method developed by the present author. The model will be first applied to analyze the cooling performance of the hybrid refrigerator with different types of phase shifting assembly. In what following, it is used to simulate the dynamic parameters in the cold stage of the pulse tube cycle. Next, optimization of the structure parameters and geometrical configuration of the new refrigerator will be presented. Finally, the influences of different hybrid regenerative materials on the cooling capacity of the new hybrid GM/PTR will be also discussed.