In recent years, the Paleogene deep exploration of Pearl River Mouth Basin has gained repeated breakthroughs, and the economic basement has been gradually lowered to more than 4 000 meters. Exploration practices show that Paleogene reservoirs of Lufeng area and Huizhou area display significant diversity and that the Paleogene reservoir in Lufeng area is better than in Huizhou area. To clarify the difference of the Paleogene reservoir between these two areas, the diagenesis of reservoir is studied by using thin section, scanning electron microscope, X-ray diffraction and physical properties analysis. According to the dissolution characteristics and dissolution products of rocks in the secondary pore development zone, the corresponding relationship between them and reservoir physical properties is established and then the pore evolution models of different types of reservoirs are restored. The research reveals that Wenchang Formation sandstone in Lufeng area, which is obviously influenced by Mesozoic sedimentary rocks,is characterized by high contents of quartz and low contents of feldspar, and mainly primary pores of pore types, develops low porosity and medium permeability or medium-high porosity and medium-high permeability reservoirs. Wenchang Formation sandstone in Huizhou area, which is obviously influenced by Mesozoic granite sources, is characterized by low contents of quartz and high contents of feldspar, mixed pores of primary pores and dissolution pores of pore types, develops medium porosity and low permeability reservoirs which could be changed into medium porosity and medium permeability reservoir refer to strong hydrodynamic force. Comprehensive study shows that the nature of parent rock determines the inherent advantages of reservoir, and that sedimentary rebuild improves the original physical property of reservoir, diagenesis difference affects the quality of reservoir. Understanding the development conditions and formation mechanism of high-quality reservoirs is of great significance for the Paleogene reservoir dessert prediction in different areas.