Miniature J-T coolers are applied extensively in electronic devices, cryosurgery and infrared detectors. The utilization of microchannels in miniature J-T coolers can induce a noticeable pressure drop through the recuperative structure, leading to modifications in the refrigeration mechanism. This study delves into the performance and coupling mechanism of throttling and heat exchange. Herein, a microchannel cooler with a noticeable throttling effect throughout the refrigeration process serves as a prototype. The mathematical model is proved with the experiments, thereby exposing limitations in the improvement of the throttling mechanism and the thermodynamic process. The analysis reveals that the backflow exhibits a significant pressure reduction (ΔPl); thus, the utilization ratio of the throttling effect is low. Additionally, further optimization of the thermodynamic process is possible by regulating throttling distribution. The performance and coupling mechanism of throttling and heat exchange with constant working conditions are investigated. The findings reveal that an optimal ratio of ΔPl (14.3 %) yields the lowest cold terminal temperature, which is reduced by up to 38.9 K. In this case, the J-T efficiency and the effectiveness of the recuperative process are observed to peak at 56.7 % and 83.8 %, respectively, indicating the optimal use of the throttling effect and interaction effects. The analysis also suggests that the thermodynamic process has been improved.