It is proved by practice of exploration that the Shizigou Paleogene reservoir contains abundant hydrocarbon resources, but deep oil-gas exploration didn’t make a big breakthrough, and the major reason is that, a poor understanding of hydrocarbon accumulation stages restrains the accurate research about accumulation process. In this paper, through the microscopic observation, fluorescence analysis and homogenization temperature and salinity test of fluid inclusions in Paleogene reservoirs of study area, the hydrocarbon charging history of Paleogene reservoir have been discussed. The result shows that there are two major stages. By integrating with the study on the burial and thermal history, the first change occurs in middle Pliocene(12-10 Ma bp) and the entrapped fluid inclusions are mainly consisted of liquid hydrocarbon and gas-liquid hydrocarbon with buff-yellow and yellow-green fluorescent light. The second time occurs in the final stage of Pliocene (4-2 Ma bp) and the entrapped fluid inclusions are mainly consisted of gas-liquid hydrocarbon with yellow-green and green fluorescent light. In addition, the reservoirs in study area also have the characteristics of multi-stage charging and continual charging, but major fluid injection time is in the later period on the whole. Therefore, the scale of later hydrocarbon accumulation is larger.