Abstract: Based on observation of casting thin section, physical properties of palaeogene Ed3 and Esl from No.3 structure of Nanpu sag are studied through longitudinal section research. Results show that the primary porosity content in Ed3 and Esl from No.3 structure of Nanpu sag exceeded 50% and the highest was more than80%. The genesis of abnormally high primary pore zone is investigated through its controlling factors based on deposition, diagenesis, hydrocarbon-charging and formation pressure. Results show that the favorable sedimentary facies belt provide a physical basis for abnormally high primary pore zone. Dissolution of silicate minerals as feldspar and rock debris is constructive to the formation of effective reservoir. Early hydrocarbon charging protects the reservoir pore, while the anomalous pressure in an early stage reduces the compaction and protects primary pores.