Petrological analysis, thin-section observation and laboratory analysis data were selected to systematically study the physical and diagenetic features of the first member of the Paleogene Shahejie Formation (Es1) in the No. 3 structural belt of the Nanpu Sag, Bohai Bay Basin. The intensities of different diagenetic processes were determined, the diagenetic evolution sequence was reconstructed, the typical diagenetic facies were identified and the effects of different diageneses on the reservoir were quantitatively analyzed. The results show that the main intergranular fillings include authigenic-quartz, quartz secondary enlargement, clay minerals, carbonate cement and matrix. The pore types include intergranular porosity, dissolution porosity and microfractures. The reservoir has experienced compaction, early cementation, dissolution and late cementation, among which compaction is the most important porosity reducer. Compaction was the main diagenetic process involved in porosity reduction, accounting for about 24.4% of the loss of thin-section porosity. The dissolution process clearly improved the porosity, increasing thin-section porosity by 2.7%. Five diagenetic facies were identified on the basis of petrographic analyses, namely, (a) strongly compacted-weakly cemented-weakly dissolved facies; (b) weakly compacted-strongly cemented-weakly dissolved facies; (c) moderately compacted-moderately cemented-weakly dissolved facies; (d) strongly compacted-weakly cemented-moderately dissolved facies; and (e) strongly compacted-weakly cemented-strongly dissolved facies. According to the analysis of diagenesis intensity, the porosity evolution model of various diagenetic facies was reconstructed, and the reservoir quality of various diagenetic facies was quantitatively predicted. The reservoir quality of different diagenetic facies clearly changed with depth. The best reservoir quality was in strongly compacted–weakly cemented–strongly dissolution facies, which have good sorting, contain a large amount of feldspar and soluble debris, and are mainly developed in the main part of the river channel. Our study can provide a reference for the subsequent exploration and development of deep petroleum systems.