Embankment–bridge transition sections (EBTSs) suffer from diverse engineering diseases that have escalated into one of the most severe issues along the Qinghai-Tibet Railway (QTR). Nevertheless, the causes and mechanisms of engineering diseases in EBTSs remain limited. This study employed a methodological approach to conduct field surveys in the Tuotuo River Basin in the hinterland of the Qinghai-Tibet Plateau (QTP). Borehole investigations and nuclear magnetic resonance (NMR) techniques accurately determined the permafrost characteristics, enabling the correction of electromagnetic wave velocity and acquisition of resistivity threshold. Ground-penetrating radar (GPR) and quasi-3D electrical resistivity tomography (ERT) were combined to indicate permafrost resistivity above 200 Ω-m. It reveals that the permafrost is relatively stable across a large area on the shaded side, whereas the permafrost degradation is more pronounced on the sunny side, where the maximum active layer thickness (ALT) reaches 5.2 m. Notable permafrost degradation and substantial increases in ALT were observed near the EBTS resulting from heat absorption and thermal erosion of the groundwater. Terrestrial laser scanning (TLS) captured time-series deformation highlights the specific displacements of the EBTS, demonstrating that the displacement is the rotational behavior of wing walls. The severe heat absorption and groundwater thermal erosion around the EBTS result in permafrost degradation and the expansion of the thawing bulbs to increased structural deformation and even failure. It was shown that permafrost degradation, moisture influence, and heat transfer characteristics are the primary contributing factors to the disease's continued deterioration, and thus reinforcement measures for existing structures need to address these three issues. The mechanisms of disease development revealed in this paper provide new insights into EBTS dynamics for the EBTS design and maintenance in permafrost regions.