The resilient modulus (M-R) used for characterization of subgrade elastic support performance is an important parameter significantly affected by matric suction after traffic opening. To investigate the correlation between resilient modulus and matric suction, soil-water characteristic curve (SWCC) and repeated load triaxial (RLT) tests for three kinds of compacted clay soils were conducted, and then the prediction model of resilient modulus considering the effect of matric suction was proposed based on effective stress theory of unsaturated soils. Test results show that the resilient modulus has a good non-linear relationship with matric suction, which can be presented by an exponential function. When the gravimetric moisture content increases from 4% below optimum water content (OMC) to 4% above OMC, M-R decreases by 29.1%-39.0% resulting from reduction of matric suction. Within the transition zone at SWCC, the prediction model with effective stress factor related to the degree of saturation can explain the contribution of matric suction to resilient modulus, and the model has higher predicting accuracy compared with the models with effective stress factor dependent on residual water content or air-entry value. With the same degree of saturation, the contribution of matric suction to effective stress is less significant with higher clay particle content and plastic index.