This study aims to overcome the technical bottleneck of non-invasive differentiation between the rammed earth layer and pebble layer in complex shallow subsurface environments, particularly focusing on the challenge of detecting highly heterogeneous pebble layers with complex wavefield characteristics. Using the western city wall of the Baodun site (Xinjin, Sichuan, China) as a case study, we introduce a high-resolution seismic detection technique combined with controllable high-frequency seismic source excitation to investigate the response characteristics of high-frequency components and energy variations of seismic waves in different strata, thereby revealing differences in physical properties between the rammed earth layer and pebble layer. Through high-frequency data acquisition, specialized processing, and interpretative analysis of seismic data, we successfully distinguish the two strata and delineate pebble-related anomalous zones. The results also indicate that, due to complex geological conditions, the reflection and refraction patterns of seismic waves in the pebble layer are exceptionally intricate. Moreover, the interplay of abrupt seismic velocity variations, interference waves, and other contributing factors leads to pronounced heterogeneity and strong scattering characteristics in the seismic data across the time, frequency, and phase domains. This research overcomes the limitations of conventional geophysical methods and confirms the applicability of high-frequency seismic techniques to complex near-surface archaeological contexts. It provides robust scientific support for the archaeological study of the Baodun site and offers a methodological reference for subsurface mapping of pebble layer in prehistoric urban landscapes.