Subgrade resilient modulus (ER) is a crucial parameter for pavement design and evaluation with a mechanistic-empirical method. To existing pavement overlaying and reconstruction, ER is difficult to determine because it is a function of both water content and stress level. In this paper, a 3-stage method to determine ER considering moisture condition coupled with stress is presented. Firstly, the equilibrium moisture of every sublayer of an existing subgrade was predicted by soil water characteristic curve and validated by in-situ water content tests. Secondly, a constitutive model of resilient modulus (MR) was established for the subgrade soil on the basis of triaxial repeated loading tests. Its parameters related to water content were regressed as well. Finally, according to the equivalent principle of deflection at the top of pavement structure, a prediction function of subgrade ER was proposed based on moisture-stress coupling condition and KENLAYER pavement analysis program. Its validity was verified by Falling Weight Deflectometer (FWD) tests. The presented 3-stage method has successfully been applied to predict ER of the existing subgrade in widening engineering of Shanghai A11 Expressway.