The conventional Joule-Thomson cooler is not compact in heat exchanger and insufficient in cooling capacity, which is limited in applying integrated electronics. However, microchannels with pillars are effective in increasing the area to volume ratio and enhancing heat transfer through the presence of vortex. Besides, multilayer microchannels are essential to enlarge the mass-flow rate in the cooler. In this study, a multilayer distributed J-T cooler with pillars is investigated. A new mathematical model of the cooler is developed and validated against the experimental data; the relative errors of the temperature and mass-flow rate are both within 5%. Furthermore, the distribution of temperature and pressure in the microchannel is analyzed by the model calculation. Numerical results show that the temperature of the high-pressure fluid decreased slightly under the influence of the heat exchange and distributed J-T effect. When the inlet pressures are 3.00, 4.00 and 5.40 MPa, the cold-end temperatures are 233.0, 185.8 and 161.2 K, respectively, with the cooling capacity reaching 2.25, 3.40 and 3.87 W, respectively. In addition, the influences of the axial heat conduction and heat leakage on the cooling performance are analyzed by using the models. The temperature rise of the cold end increases by 6.8 and 6.2 K at 5.40 MPa, respectively, considering the above two factors. The simulation model provides a useful tool for the J-T cooler.