It is reported that an unexpected breakdown occurs in reciprocating hydrogen compressors. Although the monitoring and the regular maintenance are carried out to avoid these accidents, the investigation about a trouble part is necessary to improve efficiency and safety. Previous research has shown that, the natural vibration characteristic of a system influences on the dynamic characteristic of operation. The purpose of this research is to examine the effect of stiffness change in the sliding part both on the crosshead-piston and the rod-piston system. Hence, vibrational experiments are conducted under two kinds of boundary conditions.The stiffness of the supporting points' about the crosshead and the piston are identified based on a beam model. As a result, it is found that, estimation of the system's boundary condition is possible using an identified dynamic model' s characteristics .