In order to study the characteristics of subsidence and the difference between each tectonic unit and time as well as its affecting factors in Pearl River Mouth Basin, the authors chose 32 simulation wells to calculate the subsidence and to make comprehensive analysis, and selected 12 typical wells from 32 simulation wells to make contrastive analysis. In the meantime, 3 typically evolution sections were also analyzed comprehensively. According to the results obtained, the overall subsidence can be divided into three episodes:the first episode was Eocene, whose average overall subsidence rate was 85m/myr; the second episode was from Oligocene to Middle Miocene, whose average overall subsidence rate was 146m/myr; the third episode was from Late Miocene to Quaternary, whose average overall subsidence rate was 104m/myr. The subsidence and evolution characteristics of various tectonic units were different during the same period, and the characteristics of subsidence and evolution in the same unit were also varied during different periods. The subsidence rate on the same plane can be arranged into different zones. The diversity in the changes during the subsidence evolution was affected by tectonic evolution stages of the basin as well as the structural characteristics. The characteristics of overall subsidence were controlled by basin dynamics, whereas the differences of subsidence were controlled by dynamics and structural framework. The overall subsidence can be divided into several episodes in Pearl River Mouth Basin. The characteristics of subsidence and evolution were varied between different time and space spans. Both of the basin dynamics and structural framework controlled the features of subsidence.