To optimize a research method used for fault activity intensity in petroleum basins, this study analyzed commonly used parameters to study fault activity intensity, including fault growth index, fault throw, and the rate of fault activity. Then, the new approach was used to calculate the fault throw and the vertical rate of fault activity by the differential tectonic subsidence on both sides of the fault. The characteristics of the Paleogene basement faults’ activity in the Qiongdongnan Basin were studied using the new approach. The results show that the activity of the Paleogene basement faults in the Qiongdongnan Basin can be divided into three phases.