The Jingzhushan Formation, a typical post-collisional continental molasse within the Bangong–Nujiang Suture Zone (BNSZ) of the Tibetan Plateau, preserves important evidence related to the closure of the Tethys Ocean and the collision between the Lhasa and Qiangtang terranes. However, key aspects such as its depositional age, sediment sources, and burial history remain poorly constrained, limiting our understanding of the tectonic evolution of this region. In this study, we conducted an integrated analysis of the Puga Jingzhushan section in Nyima County, combining field stratigraphy, detrital zircon U–Pb geochronology, cathodoluminescence (CL) imaging, stable isotope analysis, and clumped isotope (Δ47) thermometry, supplemented by solid-state reordering modeling. Detrital zircon U–Pb results indicate that the Jingzhushan Formation began depositing at approximately 94 Ma, with sediments mainly derived from Early Cretaceous magmatic rocks in the North Lhasa Terrane and limestone of the Langshan Formation. Clumped isotope temperatures (ranging from 51.9 to 79.2°C) are higher than expected primary depositional temperatures, indicating significant post-depositional thermal alteration. Solid-state reordering modeling constrains a maximum burial temperature of ~172°C, attributed to the combined effects of sedimentary burial and magmatic activity around 88 Ma. Furthermore, different fossil types (Auroradiolites, Eoradiolites, Sauvagesia) exhibit distinct diagenetic pathways, influenced by variations in shell microstructure, leading to either C–O bond reordering or closed-system recrystallization. We conclude that the Jingzhushan Formation was deposited in a continental setting following the Lhasa–Qiangtang collision. Its burial and exhumation history reflects Late Cretaceous tectono-magmatic interactions, offering new thermochronological insights into early uplift and tectonic transition in central Tibet.