To address the uncertainty of optimal vibratory frequency fov of high-speed railway graded gravel (HRGG) and achieve high-precision prediction of the fov, the following research was conducted. Firstly, commencing with vibratory compaction experiments and the hammering modal analysis method, the resonance frequency f0 of HRGG fillers, varying in compactness K, was initially determined. The correlation between f0 and fov was revealed through vibratory compaction experiments conducted at different vibratory frequencies. This correlation was established based on the compaction physical–mechanical properties of HRGG fillers, encompassing maximum dry density ρdmax, stiffness Krd, and bearing capacity coefficient K20. Secondly, the gray relational analysis algorithm was used to determine the key feature influencing the fov based on the quantified relationship between the filler feature and fov. Finally, the key features influencing the fov were used as input parameters to establish the artificial neural network prediction model (ANN-PM) for fov. The predictive performance of ANN-PM was evaluated from the ablation study, prediction accuracy, and prediction error. The results showed that the ρdmax, Krd, and K20 all obtained optimal states when fov was set as f0 for different gradation HRGG fillers. Furthermore, it was found that the key features influencing the fov were determined to be the maximum particle diameter dmax, gradation parameters b and m, flat and elongated particles in coarse aggregate Qe, and the Los Angeles abrasion of coarse aggregate LAA. Among them, the influence of dmax on the ANN-PM predictive performance was the most significant. On the training and testing sets, the goodness-of-fit R2 of ANN-PM all exceeded 0.95, and the prediction errors were small, which indicated that the accuracy of ANN-PM predictions was relatively high. In addition, it was clear that the ANN-PM exhibited excellent robust performance. The research results provide a novel method for determining the fov of subgrade fillers and provide theoretical guidance for the intelligent construction of high-speed railway subgrades.