Frost formation degrades the performance of heat exchangers greatly, thus influencing the cryogenic refrigerator. Different from frost formation on the evaporator surface, the growth and migration of frost layer inside the heat exchanger is of low temperature and humidity. In addition to the constantly changing boundary conditions, the effective prediction is difficult. In the present study, a numerical model was proposed to analyze the frost formation in the cryogenic heat exchanger of a reverse Brayton air refrigerator. Under small amounts of moisture, the growing of frost layer was simulated through the numerical heat and mass transfer by adopting semiempirical correlations. The frost formation model was inserted into the transient model of refrigerator, and numerical calculations were performed on heat and mass transfer rates, and growth and migration of frost layers in forced convection conditions. Experiments were conducted under different air humidity to investigate the frost formation and verify the numerical model. Through the model, the influences of frosting on the refrigerator were evaluated under different moisture contents and running time. It can be used to predict the performance of air refrigerators with low humidity and provide a basis for improving the system operation and efficiency.