In an extensional basin, the surface thermal flux could be controlled by several factors such as the thermal flux derived from mantle, radioactive heat generation of the upper crust and sediments, and the thermal conductivities of lithosphere and sedimentary strata. According to the thermal conduction theory, this paper analyzes the surface thermal flux distribution and its ideal relation with the extension factor in the process of basin evolution within the pure-shear model. As a result, the surface thermal flux in an extensional sedimentary basin is always dominated by the energy of deep thermal sources, extension factor, radioactive heat generation in the upper crust and also the structural position in the basin. In combination with the real geologic phenomena during the basin evolution such as thermal conductivity of sedimentary strata, magma underplating and volcanism, this paper improves the traditional pure-shear model. Then the current surface thermal flux distribution in the Jiyang depression in the Bohai Bay basin is inversed. The result is quite similar to that calculated by forward methods. Using an improved pure -shear stretching model, the surface thermal flux variations during multiple episodes of extension in the Jiyang depression are also simulated. This inversion method provides an efficient way to research the basin thermal evolution and evaluate petroleum resources quantitatively, especially is suitable to the area lacking geologic data.