The stretching process of some Tertiary rift basins in eastern China is characterized by multiphase rifting. A multiple instantaneous uniform stretching model is proposed in this paper to simulate the formation of the basins as the rifting process cannot be accurately described by a simple (one episode) stretching model. The study shows that the multiphase stretching model, combined with the back-stripping technique, can be used to reconstruct the subsidence history and the stretching process of the lithosphere, and to evaluate the depth to the top of the asthenosphere and the deep thermal evolution of the basins. The calculated results obtained by applying the quantitative model to the episodic rifting process of the Tertiary Qiongdongnan and Yinggehai basins in the South China Sea are in agreement with geophysical data and geological observations. This provides a new method for quantitative evaluation of the geodynamic process of multiphase rifting occurring during the Tertiary in eastern China.