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A low‐viscosity crustal layer (LVCL) due to partial melt and/or hydration has been detected within the continental crust (e.g., in South China block), but its role in the development of hyperextended margins is still not entirely understood. Using 2‐D thermomechanical modeling, we simulate the lithospheric extension with a LVCL embedded within the continental crust. Results show that the ductile layer determines the width of highly thinned crust and the crustal thermal distribution. Detailed effects are found by varying the initial effective viscosity and thickness of the layer: (1) a rheologically weaker and/or thicker LVCL accommodates more deformation and thus results in a slow and distributed crustal thinning and (2) preferential removal of the lithospheric mantle places the crust in direct contact with the hot upwelling asthenosphere, promoting the development of highly thinned and hot continental crust. Both the widths of highly thinned crust and the thermal values increase when the rheology of the ductile layer decreases or the thickness increases. Furthermore, we obtain the crustal thickness and geothermal characteristics of the northern South China Sea (SCS) margin using reprocessed geophysical data and newly complied heat flow data. A detailed comparison of our modeling results with the northern SCS margin suggests that variation in the LVCL thickness may be a possible mechanism for the differential width of highly thinned crust and high heat flow zone along strike of the northern SCS margin.