Geosynthetic reinforced pile-supported (GRPS) embankment is widely used in the construction of high-speed railways on soft foundations. Arching effect, which is a common phenomenon in the system involving soil-structure interaction, is considered a key factor in the design of GRPS embankment. Its performance has been found inevitably to affect the post-construction settlement and bearing capacity of the embankment. However, the existing design methods are mainly based on static loading condition; soil arching effect under high-cycle loading has not been fully understood. In this study, a series of numerical simulations were conducted to study the long-term behavior of GRPS embankment under traffic loading, with the consideration of arching effect in soil. An implicit–explicit transition calculation algorithm was implemented to predict the permanent deformation under high-cycle traffic loading through the data transfer and conversion between implicit and explicit numerical stages, in which the mixed “implicit” and “explicit” calculation strategy were carried out based on the high-cycle accumulation (HCA) model. By using the proposed algorithm, a cross-section of high-speed railway GRPS embankment was selected as a case for discussion. Results indicate that the affected areas of stress concentration over piles in the embankment are reduced under traffic loading. With different levels of stability, the variation of stress concentration ratio of the arching effect can be mainly classified into three groups: stable, gradually weakened, and destroyed. Through parameter study, the effect of subsoil stiffness is discussed and a reasonable modulus ratio between pile and subsoil is suggested for the design reference.