In addressing the critical need to understand the geological and diagenetic factors affecting Paleogene sandstone reservoirs in the Baiyun Sag—a region vital for oil and gas exploration—this study delves into the Paleogene Zhuhai and Enping formations. Advanced methodologies, including petrographic thin-section analysis, scanning electron microscopy, wavelet analysis, and carbon and oxygen isotope analysis, were employed to evaluate their petrological characteristics, pore structures, physical properties, and key diagenetic processes. The results indicate that the Zhuhai Formation is primarily composed of feldspathic quartz sandstones with prevalent intergranular dissolution pores, while the Enping Formation consists mainly of feldspathic sandstones with intragranular solution pores. The diagenetic temperatures across both formations ranged from 42.6 to 116.3 °C. The studied reservoirs have experienced porosity alterations due to mechanical compaction (23.07% reduction), carbonate cementation (9.02% reduction), and dissolution (5.09% enhancement). Notably, feldspar dissolution emerged as a significant contributor to high-quality reservoirs, particularly in the upper Enping Formation. These findings offer invaluable insights into the diagenetic evolution of sandstone reservoirs in the Baiyun Sag and hold significant implications for guiding future oil and gas exploration efforts in the region.