Due to entire pneumatic connection between free piston and free displacer, the motion parameters of them including amplitude and phase shift can actually impact the cooling capacity and overall performance of cryocooler obviously. In this study, the procedure of design and manufacture pneumatic free piston and free displacer (FPFD) Stirling cryocooler had firstly been described in details. Then in order to accomplish study, the experimental bench has been set up based on 80 K@1 W Stirling cryocooler. The effect of the thermodynamic and pneumatic parameters including charging pressure, natural frequency of displacer, damping coefficient of displacer, working frequency on the pressure, displacement and displacer phase shift has been investigated, respectively by means of experimental and theoretical method. In particular, the variation of damping is realized by adjusting the width of clearance cut on the additional damping component, which is screwed on the displacer rod. Similarly, natural frequency of displacer is changed by the extra mass connected on the displacer. Due to the results of experimental study, the optimum working conditions of this Stirling cryocooler for 80 K cold tip temperature are as follows: charge pressure 15 bar, natural frequency of displacer 46 Hz, width of clearance 300 μm and working frequency 43 Hz. In agreement with the optimum working conditions, neighborhood interval of 90° is the ideal working domain for displacement phase shift. Meanwhile, the displacer phase shift should approach to 0°as near as possible and pressure phase shift should also be as small as possible, which have linear relation with non-dimensional damping characteristic of compressor. In view of theoretical study, the expressions of three phase shifts deduced from thermodynamic equation of piston and displacer respectively are expressed as the functions of working parameters, which are verified by the experimental data and consequently can be used as the powerful guidance to optimum seeking.