Thermal history reconstruction of deep, lithologically diverse strata (>4500 m) in sedimentary basins remains challenging because of the limited availability of reliable paleo-thermal indicators. In this study, we develop an innovative methodological framework based on independent modeling and cross-validation of multiple thermal indicators, integrating carbonate clumped isotope (Δ47) thermometry, in situ U–Pb geochronology, and zircon (U–Th)/He (ZHe) thermochronology to reconstruct the thermal evolution of deep, heterogeneous strata in the Tarim Basin, Northwest China. The measured TΔ47 values of micrite, calcite vein, and dolomicrite samples from Cambrian‒Ordovician strata in the Tabei Uplift range from 75.8 °C to 108.6 °C, while corresponding in situ U–Pb ages cluster between 463 ± 8 Ma and 495 ± 48 Ma, consistent with depositional timing. Single-grain ZHe ages from clastic rock samples range from 17.2 Ma to 472.3 Ma and are uniformly younger than their stratigraphic ages, indicating complete post-depositional He diffusion and suitability for thermal history modeling. Thermal histories reconstructed from the integrated, independently modeled thermal indicators reveal peak burial temperatures of approximately 135‒210 °C since the Neoproterozoic, attributable to post-orogenic rapid sedimentation, mantle plume activity, and magmatic intrusions. Three distinct thermal evolution patterns are identified across the Tabei Uplift, leading to differential source rock maturation trajectories and hydrocarbon charging histories. The long-term low-temperature yet high-pressure conditions preserved in superdeep formations of the Tabei Uplift provide favorable conditions for liquid hydrocarbon preservation, highlighting substantial petroleum potential at great depths. Overall, this study demonstrates the robustness of a multi-indicator, cross-validated thermal reconstruction strategy and provides critical constraints on the thermal evolution of deep, diverse strata, with important implications for hydrocarbon preservation and phase behavior in superdeep reservoirs.