The reservoir of Wenchang Formation in Huizhou Sag is the key exploration strata of Paleogene in Pearl River Mouth Basin. Based on the data of thin section, scanning electron microscope and properties, this paper studied the petrologic characteristics, reservoir space, pore structure, properties and main controlling factors of the reservoir of Wenchang Formation in Xijiang-Huizhou transform zone. The result shows that pore types are mainly intergranular corrosion expansion pores and primary intergranular pores, and a great deal of kaolinite was precipitated in corrosion pores and primary pores and produce intercrystalline pores in some strata. The pore structure is better in the reservoir which the intercrystalline pores are not developed. The content of clay, carbonate and feldspar in the fillings are the main controlling factors. The crush fracture formed by compaction is the major contribution to the permeability of deep reservoir. The clay film of the illite-smectite mixed layer which is formed early can resist the compaction and inhibit the corrosion on the grain, preserving some intergranular pores.