Mesozoic-Palaeozoic marine carbonate rocks are important hydrocarbon reservoirs in the Central Uplift area of the South Yellow Sea Basin (SYSB). Due to the lack of boreholes and the great heterogeneity of carbonate reservoirs, the distribution of porous carbonate reservoirs and their related key controlling factors remain unclear. Based on seismic inversion and isotope analysis, this study explores the factors affecting the distribution of porous Carboniferous-Early Permian carbonate reservoirs in the SYSB. In this study, the log-seismic characteristics of porous carbonate reservoirs, sensitive lithology parameters, and physical property parameters are extracted and analyzed. The pre-stack simultaneous inversion technique is applied to predict the lithology properties and physical properties of the porous carbonate reservoirs. Moreover, the sedimentary of carbonate is analyzed using isotopes of carbon, oxygen, and strontium. The results indicate that porous carbonate reservoirs with porosities of 3%~5% mainly occur at the paleo-highland (Huanglong Formation and Chuanshan Formation) and the slope of paleo-highland (Hezhou Formation). The porous carbonate reservoirs of the Qixia Formation are only locally developed. In addition, the study area was dominated by a warm and humid tropical climate from the Carboniferous to Early Permian, with four sea-level eustatic fluctuation indicated by the negative and positive δ13C excursions. When the sea level fell, the study area was exposed and denuded, and the supply of terrigenous detrital was dominated, which significantly influenced the carbonate deposit and diagenesis. This study highlights that sedimentation was a key factor in controlling the quality of Carboniferous-Early Permian carbonate reservoirs. The methods proposed in this study can be used in other carbonate-dominated strata worldwide.