The recuperative matrix heat exchanger (MHE) has advantages of large specific surface area, compactness, high effectiveness, and low flow resistance, which make it promising for applications in Joule-Thomson cryocooler and reverse Brayton cryocooler. In this study, a numerical model is developed to predict the thermal performance of MHEs. The effects of axial conduction of both inner and outer walls as well as radial heat conduction through mesh-screens and the heat leakage are considered. The temperature distribution over the fluids and mesh screens in MHEs can be determined using this model. The model is validated by analytical solution of effectiveness-NTU method and the results of the experimental tests on two MHEs with different structures at cryogenic temperature. Using the proper correlations for heat transfer coefficients, the relative deviations of the ineffectiveness predictions from experimental results are below 13.2% in the mass flow range of 0.4 g/s – 2.1 g/s. The numerical results show that the axial conduction of inner and outer walls has similar effects on the thermal performance of MHEs. The increase of axial conduction can substantially lower the effectiveness of the MHEs at mass flow rates below 1 g/s, while the influence of the number of transfer unit (NTU) on the MHE effectiveness becomes dominant at mass flow rates above 1 g/s.