The quantitative grain fluorescence and quantitative grain fluorescence on extract have become effective approaches in the analysis of hydrocarbon evolution in clastic reservoirs recently. The cutoff threshold for differentiating current/paleo-oil and water zones is crucial to reconstruct accurately hydrocarbon accumulation history. However, the absence of theoretical study on the cutoff threshold in the carbonate reservoir has precluded their application and development. In this paper, we attempted to investigate the cutoff threshold by analyzing the quantitative grain fluorescence and quantitative grain fluorescence on extract parameters and spectra of the cores and natural carbonate outcrop samples in known current/paleo-oil and water zones revealed by the frequency of oil inclusions, formation test, logging analysis, etc. Based on this, the hydrocarbon charging history of the Suqiao Buried-hill Zone, Bohai Bay Basin, eastern China was reconstructed using the gotten threshold. Results show that the carbonate minerals fluorescing will lead to a higher cutoff threshold of quantitative grain fluorescence index value in the carbonate reservoir, while the threshold of quantitative grain fluorescence on extract intensity value is coincident with the corresponding value in the clastic reservoir. The quantitative grain fluorescence and quantitative grain fluorescence on extract data have unraveled a complicated hydrocarbon accumulation history in Suqiao Buried-hill Zone including oil charging before gas and paleo-oil loss due to the tectonism. The ascertained cutoff threshold in this study is of great significance for reconstructing accurately and effectively the complicated hydrocarbon charging history in the carbonate reservoir, which provides significant models for future petroleum exploration.