The carbonate reservoirs of Cenomanian–Early Turonian in the northeastern Central Arabian Basin hold considerable oil reserves and are great contributors to oil production. Diagenesis have a great impact on carbonate reservoir petrophysical properties, microstructure, and heterogeneity. By integrating cores, cast thin sections, regular core analysis, CT, and isotopes, this study provides an improved understanding of diagenesis in the Cenomanian–Early Turonian and its effect on carbonate reservoirs. The results showed that three diagenetic environments were identified in the Cenomanian–Early Turonian based on texture, structure, cement, crystal form, and crystal size, which were marine environment, meteoric environment, and burial environment. Six diageneses were identified based on residual bioclastic, secondary pores, calcite quantity, dolomite size, and stylolite, namely dissolution, cementation, micritization, dolomitization, compaction, and pressure solution. A micritization model in high energy sediment, a dolomitization model in burrows, and a comprehensive diagenetic model were established. It concluded that dissolution during meteoric environment is most favorable to reservoir physical properties, while cementation is least favorable. The cement content controls the microstructure and petrophysical property. Micritization is detrimental to the petrophysical properties, and the micrite it forms are distributed in the interparticle pores, reducing the reservoir property deposited in high energy environment. Dolomitization is less developed in substrate but widely developed in burrows, which result in the physical properties of the burrows being higher than those of substrate. Compaction and pressure solution have a negative impact on reservoir physical properties.