Abstract: This study addresses discrete foundation treatment problems in soil–rock mixtures by proposing a pneumatic vibratory probe compaction method based on the Brazil nut effect, filling the theoretical gap in engineering applications of BNE for ground improvement. Through the integration of a 120 kW variable-frequency vibration hammer with 3 MPa high-pressure gas jet technology, a dual-mode energy regulation strategy of "high-frequency, high-pressure penetration – low-frequency compaction" was established, verifying the effect of vibration parameters on structural reconfiguration of the discrete medium. Field experiments demonstrated that a vibration intensity Γ > 4.77 (frequency ≥10 Hz, amplitude = 12 mm) effectively activates BNE. The 15 Hz high-frequency vibration increased dynamic penetration count in shallow layers by 275.6%, while reducing lifting speed to 0.2 m/min significantly enhanced coarse particle enrichment compared with high-speed lifting. Post-treatment foundations achieved a bearing capacity characteristic value of 476 kPa, with additional collapsibility ΔFs reduced from 108.61 mm to 3.96 mm. The research confirms that this method induces structural segregation and reconstruction through vibration energy, forming a dual-layer architecture characterized by an interlocked coarse-grained framework in the upper part and densely compacted fine particles in the lower part, thereby providing theoretical support and an engineering paradigm for heterogeneous foundation treatment with stone content below 60%.