The reciprocating flow in an Inertance Pulse Tube Cryocooler (IPTC) with the piston movement in a compression chamber was modeled numerically and analyzed. The numerical modeling on the axisymmetric two-dimensional thermal fluid motion was applied to the reciprocating flow in an IPTC and compared the transient velocity field and temperature in the IPTC. The modeling of IPTC consists of the flow and heat transfer in the cylinder of compressor, a regenerator with a porous media, a pulse tube, 2 heat exchangers with a porous media, a long inertance, and a reservoir. The crevice between free piston and cylinder wall in the compressor was also modeled to consider the effect of leaked gas through the crevice during compression and expansion of cylinder volume. It is investigated the effect of volume ratio between the back space of piston and the compression space on the cooling performance or energy efficiency of IPTC was investigated with the temperature and flow distribution.