When tunnels pass through collapsible loess layers, rainfall infiltration and construction disturbances will easily lead to engineering failures such as instability, large deformation and landslide. Therefore, it is very necessary to research on the effect of rainfall infiltration on the stability of shallow loess tunnels. The elastic-plastic incremental constitutive relation of undisturbed soil was established based on the loess triaxial test and the analysis of experimental data. Then, the elastic-plastic incremental was applied in Midas software to analyze the tunnel stability of the shallow section when the rainfall infiltration was considered in some loess tunnel. Finally, numerical simulation results of the deformation and stress conditions are compared before and after the rainfall infiltration. The results are shown as follows: The increase of water content has great influence on loess mechanical properties and damage morphology. When considering rainfall infiltration, the deformation of tunnel and the stress of preliminary support structure are significantly increased. In this situation, the settlement of the tunnel vault increases 46% and the stress of preliminary support structure increases 20%~27%. The results show the elastic-plastic incremental constitutive relation is reasonable and results of the numerical simulation is reliable with comparing the calculated and measured data of tunnel deformation. The research conclusions in this paper have certain reference value for the design of support parameters and construction technology in loess tunnels.