Conventional subsidence analysis methods are generally based on the assumption of instantaneous stretching, which totally ignores the heat loss during continental rifting. For long-duration or multi-episodic extensional tectonics, such assumption is no longer valid and could cause significant deviation from real subsidence. Here I extend original finite stretching model to a multi-stage scenario in terms of geothermal and structural successions between two adjacent rifting events. A procedure is designed to estimate stretching factor by fitting the whole tectonic subsidence history in a self-consistent manner on the basis of the extended model. I apply this procedure to the Baiyun Sag in the continent slope of the South China Sea. Subsidence analysis shows that the sag is characterized by two episodes of rifting. The first stage (49 to 23.8 Ma) resulted in stretching factors in the range of 1.3 to 4.0 with the greatest stretching at the sag center, while the second one (17.5 to 10.5 Ma) yielded minor stretching factors of 1.1 to 1.2. These estimates agree well with that determined from crustal thinning for the northern and central potions of the sag, but significant discrepancy occurs between the southern edge of the sag and the present continent–ocean boundary, where the crustal thickness is less than 20 km and potentially extensive magmatic intrusion was well imaged in the seismic profiles. I suggest that the magma-assisted rheologically weakening and possible lower crust ductile flow contributed to the extension discrepancy. The margin north of the Baiyun Sag, having a relatively thick crust and vacant of magmatic activity, was basically stretched in a depth-uniform style. It is inferred that preexisting weakness in the lithosphere and abundant sediment supply were responsible for the extremely thick Cenozoic sediment developed in the Baiyun Sag.