With the accelerated advancement of smart city construction, the development of urban underground space in coastal areas faces significant safety challenges due to randomly distributed granite boulders. Conventional geophysical methods often struggle to identify these heterogeneous bodies efficiently. This study proposes a comprehensive detection approach fusing the Cone-based Transient Electromagnetic Method (CTEM) and Microtremor Array Surveying. Taking the eastern coast of Jiaozhou Bay, Qingdao, as the research area, we integrated borehole data to validate the geophysical interpretation. The results demonstrate that the joint inversion accurately delineates four stratigraphic interfaces with depths consistent with borehole logs: the artificial fill (bottom at ~8–12 m), Quaternary sediments (~28–33 m), strongly weathered granite (~59–74 m), and moderately weathered granite. Specifically, boulders within the Quaternary and strongly weathered layers are distinctly identified by dual high-value anomalies: high apparent resistivity (>220 Ωm, approximately 1.5–2 times that of the surrounding rock) and high shear-wave velocity (>660 m/s). Furthermore, the method effectively differentiates boulders from water-rich fractured zones, which exhibit contrasting low resistivity (<50 Ωm) and low shear-wave velocity (<420 m/s). These quantitative findings confirm that the fused CTEM and microtremor technique provides precise spatial localization and reliable identification of boulders in complex coastal geological environments.