Applying microchannels in Joule-Thomson (J-T) coolers can enhance precooling. The regulation of heat transfer and throttling is crucial to lower the cold terminal temperature Tcold.The present cooler with rectangular microchannels served as the prototype. The experiments were carried out under 4, 5 and 6 MPa, with Ar and N2 as the refrigerants. The cooler can achieve the lowest cold terminal temperature (Tcold, 194.9 K) at 6 MPa. Then, the mathematical model was verified. The analysis showed that under the premise of constant total length and working condition, the precooled temperature before throttling could be reduced, and finally, the Tcold could be reduced. There are two ways to regulate. On the one hand, extending the recuperative structure (CFHX)’s length and reducing the length and cross-sectional flow area of the throttling structure (THR). This regulation increased the heat exchange per unit mass qm and the integral throttling effect ΔTjt in each section and finally reduced the Tcold. When the length of THR was decreased to 15 mm, and the end of THR reached the chocked flow, the Tcold reached the lowest value of 166.3 K. On the other hand, when fins were added in CFHX, THR became shorter. This method enhanced the precooling at the expense of pressure drop in CFHX. When the fins’ number raised from 0 to 6, Tcold declined. When the number is 6, the Tcold decreased by 7.7 K. As the number went on rising, the performance eventually deteriorated.