The North Yellow Sea Eastern Sub-basin is a typical Meso-Cenozoic small superimposed faulted basin, currently in its early exploration phase. Comprehensive studies on the complex tectonic-thermal evolution in this region are lacking. By integrating vitrinite reflectance (R_o) and apatite fission track (AFT) analysis, the thermal history and geothermal gradient of the Meso-Cenozoic era have been reconstructed in this basin, alongside assessments of erosion thickness and processes. These investigations have enabled an analysis of the thermal evolution history of Middle-Upper Jurassic source rocks. Results indicate that paleo-heat flow peaked at 75-90 mW/m² during 120-100 Ma, decreased to 60 mW/m² at 40 Ma, and then rose to 70 mW/m² at present. Correspondingly, temperatures declined gradually from 100-70 Ma but rapidly dropped during 70-40 Ma, with the geothermal gradient shifting from 34-36 ℃/km to 23 ℃/km before rising to 28 ℃/km. Overall, paleo-geothermal gradient and heat flow were higher before the Late Cretaceous, aligning with the transition from a faulted basin to a depression basin. Intense uplift and erosion occurred during the Late Cretaceous-Eocene, resulting in an erosion thickness of approximately 1.0-1.5 km. Deposition slowed or ceased during 100-90 Ma, with significant uplift occurring during 85-40 Ma, especially rapid during 70-40 Ma. The tectonic-thermal history has influenced hydrocarbon generation, with both Middle and Upper Jurassic source rocks experiencing early hydrocarbon generation during the Late Jurassic-Early Cretaceous. In the central depression, erosion thickness was thinner in the Lower Cretaceous-Eocene, while deposition thickness was thicker in the Oligocene-Quaternary, leading to higher present-day strata temperatures and favoring late hydrocarbon generation. Exploration efforts for potential accumulation should focus on areas surrounding hydrocarbon generation depressions.