Mixed Refrigerant Joule Thomson (MR-JT) refrigerators are widely used in various kinds of cryogenic systems these days. Printed Circuit Heat Exchanger (PCHE) is one of the promising cryogenic compact recuperators for MR-JT refrigerators due to its compactness, high NTU and robustness. However, PCHE composed with microchannel bundles can cause flow mal-distribution, and it can cause the degradation of thermal performance of the system. To mitigate the flow mal-distribution problem, the cross link (or intra-layer bypass) can be adapted to parallel microchannels. Two heat exchangers are fabricated in this study; one has straight channels, and the other one has intra-layer bypass structure between channels to enhance the flow distribution. The MR-JT refrigerators are operated with these two heat exchanger and the no-load temperatures are compared. The lower no load temperature achieved with the intra-layer bypass structured heat exchanger. The results indicate that the flow mal-distribution in the microchannel heat exchanger can be mitigated with intra-layer bypass structure, and relaxation of flow mal-distribution in the heat exchanger guarantee the MR-JT refrigerator's performance.