The Neogene Sanya and Meishan formations are important sequences of source rocks in the Yinggehai Basin. Understanding the paleo-tectonic geomorphology is an important basis for predicting the distribution of source rocks and the potential of oil and gas resources. Based on the rule that "the paleo-tectonic environment develops in the inherited way when tectonic stress system remains unchanged", we applied the idea and method of "the present is the key to the past" and "proportional compensation" to interpret the Neogene tectonic deformation system and its evolution in the Yinggehai Basin. The current geomorphological features and stratigraphic thickness distribution were used with the paleo-sea depth determined from single well data as a constraint to restore the Neogene paleo-geomorphology of the Yinggehai Basin. The Yinggehai Basin was a semi-enclosed confined bay during the deposition of the Sanya and Meishan formations, which was conducive to the development of source rocks. The "proportional compensation" method, which is a new way for paleo-geomorphology restoration, can be applied in other basins.