Basin thermal evolution is an immediate dominant factor for controlling source rock evolution and gas production. Two seismic profiles, gl and g2, across the Subei Basin were studied with tectonic-thermal evolution modeling. With the aim to reconstruct the extension of the Subei Basin after Cretaceous, the thermal history was divided into three extension stages. During the first extension stage (95-83 Ma), the basement heat flows from different tectonic units in the Subei Basin were low and uniform. For the second stage (83-54.9 Ma), the basement heat flow values increased gradually, and the values started to vary between the different tectonic units. In the last stage (54.9-38 Ma), the basement heat flows increased apparently, and many heat flows reached the maximum value in this modeling, while different tectonic units revealed large differences. After the Neogene, these heat flow values of the Subei Basin were stable due to the slight tectonic inversion.