The flow characteristics of inertance pulse tube cryocooler(IPTC) was investigated with a computational thermal fluid dynamics for the reciprocating flow in IPTC including the piston movement of linear compressor. Two dimensional axisymmetric modeling was applied for the flow in an IPTC with a clearance between the piston and cylinder wall of linear compressor. The pressure, velocity, and temperature distribution were examined for the steady state. These were compared with previous results to confirm the validity in the modeling and computational results. The leakage between piston and cylinder wall affect the cooling capacity seriously. The dependence on mesh numbers were also examined to obtain a proper mesh numbers to improve the accuracy of calculation, which showed significant effect on the results. The user-defined function was used for the process of compression and expansion of piston.