This paper aimed to investigate the feasibility of partially or completely replacing natural aggregates with recycled aggregates from construction and demolition wastes for low-carbon-emission use as coarse-grained embankment fill materials. The laboratory specimens were prepared by blending natural and recycled aggregates at varying proportions, and a series of laboratory repeated load triaxial compression tests were carried out to study the effects of material index properties and dynamic stress states on the resilient modulus and permanent strain characteristics. Based on the experimental results and by considering the main influencing parameters of the resilient modulus and permanent deformation, an artificial neural network (ANN) prediction model with optimal architecture was developed and optimized by the particle swarm optimization (PSO) algorithm, and its performance and accuracy were verified by supplementary analyses. A shakedown state classification method was proposed based on the unsupervised clustering algorithm, and a prediction model of critical dynamic stress was established based on the machine learning (ML) method and the shakedown state classification results. The research results indicate that the stress state has a greater influence on the resilient modulus and permanent deformation characteristics than other factors, and the shear stress ratio has a significant effect on the shakedown state. The resilient modulus and critical dynamic stress of such specimens vary linearly with confining pressure. The improved PSO-ANN prediction model exhibits high prediction accuracy and robustness, superior to several other commonly used ML regression prediction algorithms. The resilient modulus and critical dynamic stress prediction methods based on ML algorithms can provide technical guidance and theoretical basis for the design and in-service maintenance of similar unbound granular materials.